1 /*
2 * modelmixture.cpp
3 *
4 * Created on: Nov 29, 2014
5 * Author: minh
6 */
7
8 #include "modelmarkov.h"
9 #include "modeldna.h"
10 #include "modelprotein.h"
11 #include "modelbin.h"
12 #include "modelcodon.h"
13 #include "modelmorphology.h"
14 #include "modelset.h"
15 #include "modelmixture.h"
16 #include "modelpomo.h"
17 //#include "phylokernelmixture.h"
18 #include "modelpomomixture.h"
19
20 using namespace std;
21
22 const char* builtin_mixmodels_definition = R"(
23 #nexus
24
25 begin models;
26
27 [ ---------------------------------------------------------
28 EX2 mixture model of Le, Lartillot & Gascuel (2008)
29 --------------------------------------------------------- ]
30
31 [ Exposed component ]
32 model ExpEX2 =
33 0.526738
34 0.483150 0.505837
35 0.658902 0.051052 3.902456
36 2.051872 2.214326 0.961103 0.129989
37 1.280002 2.039552 1.301786 0.399061 0.456521
38 1.306565 0.137928 0.285806 3.100403 0.033946 2.514377
39 1.370782 0.363365 1.820100 0.885317 0.886564 0.320746 0.303966
40 0.540809 2.288922 4.949307 0.700890 2.172284 3.755421 0.270957 0.401311
41 0.171986 0.237023 0.337226 0.018315 1.037046 0.212032 0.084442 0.012279 0.317239
42 0.430511 0.670514 0.158937 0.021949 1.702066 1.261113 0.110508 0.052946 0.869247 8.675343
43 0.697731 3.881079 1.677194 0.105450 0.146263 2.570254 0.730337 0.279865 0.598289 0.338782 0.313102
44 1.043937 0.656943 0.539827 0.066925 1.846562 1.973592 0.188160 0.158136 0.519993 9.483497 14.176858 1.013268
45 0.265209 0.097443 0.182522 0.026918 3.002586 0.080193 0.023999 0.084663 2.047163 2.193062 4.802817 0.044792 3.261401
46 1.270693 0.166534 0.068692 0.228829 0.156216 0.362501 0.214847 0.148900 0.323141 0.071992 0.343919 0.195470 0.099252 0.087020
47 4.826665 0.751947 4.412265 0.975564 5.294149 1.033459 0.382235 1.970857 0.993310 0.190509 0.389101 0.592156 0.557254 0.668834 1.223981
48 2.131819 0.584329 2.133604 0.368887 2.067387 1.013613 0.511390 0.174527 0.580960 2.563630 0.522334 1.147459 2.960091 0.244420 0.413148 7.384701
49 0.143081 0.475590 0.061094 0.042618 1.603125 0.210329 0.048276 0.186382 0.961546 0.208313 1.130724 0.052858 1.328785 5.210001 0.045945 0.316078 0.144393
50 0.208643 0.196271 0.599369 0.121313 3.842632 0.158470 0.064648 0.039280 8.230282 0.517123 0.713426 0.084962 0.812142 23.228875 0.043249 0.405310 0.234217 4.903887
51 2.544463 0.313443 0.172264 0.073705 4.207648 0.497398 0.484620 0.132496 0.329895 23.711178 3.466991 0.348362 4.136445 1.199764 0.368231 0.266531 3.184874 0.252132 0.459187
52
53 0.088367 0.078147 0.047163 0.087976 0.004517 0.058526 0.128039 0.056993 0.024856 0.025277 0.045202 0.094639 0.012338 0.016158 0.060124 0.055346 0.051290 0.006771 0.021554 0.036718;
54
55 [ Buried component ]
56 model BurEX2 =
57 0.338649
58 0.201335 0.981635
59 0.283859 0.247537 6.505182
60 2.640244 0.904730 1.353325 0.312005
61 0.543136 4.570308 2.439639 0.682052 0.216787
62 0.748479 0.917979 0.804756 10.030310 0.024055 8.670112
63 2.700465 0.539246 0.810739 0.810727 0.701320 0.330139 0.636675
64 0.237686 3.175221 6.308043 1.540002 0.469875 8.675492 0.750683 0.183743
65 0.044209 0.099241 0.162644 0.020816 0.166986 0.082745 0.030581 0.005017 0.075820
66 0.124047 0.314159 0.088243 0.017526 0.449241 0.641784 0.073392 0.017752 0.277023 2.383760
67 0.433721 17.781822 2.851914 0.459939 0.117548 6.815411 3.482941 0.484653 1.247888 0.161658 0.219757
68 0.497479 0.448773 0.380964 0.057176 0.815999 2.089412 0.291379 0.054491 0.307450 2.817174 4.759683 1.082403
69 0.093991 0.055530 0.098936 0.026160 0.662517 0.091948 0.022760 0.034431 0.675645 0.521416 1.672365 0.077917 1.296869
70 0.986621 0.356417 0.214521 0.246129 0.164228 0.654039 0.295079 0.179095 0.428213 0.037671 0.170780 0.347219 0.074086 0.057233
71 5.925588 0.979993 4.725421 1.158990 5.111992 1.120931 0.737456 2.279470 0.886126 0.051057 0.089611 0.925355 0.275366 0.274582 1.151114
72 1.958501 0.630713 2.007592 0.289641 2.284140 0.787821 0.539892 0.097432 0.467489 0.644041 0.202812 1.401676 1.340732 0.103118 0.601281 8.190534
73 0.068357 0.784449 0.109073 0.085810 0.457880 0.297731 0.155877 0.157418 0.708743 0.054134 0.374568 0.115777 0.477495 2.362999 0.047127 0.209085 0.097054
74 0.084768 0.312038 0.615093 0.202611 0.788164 0.293543 0.137306 0.035497 4.938330 0.101803 0.180086 0.280737 0.264540 8.142914 0.059308 0.264401 0.133054 2.905674
75 1.387752 0.140091 0.112176 0.058637 1.575057 0.203946 0.239406 0.044011 0.085226 6.427279 1.035942 0.244336 1.033583 0.278010 0.213475 0.079878 1.592560 0.081135 0.108383
76
77 0.123119 0.019475 0.019852 0.018583 0.018711 0.017275 0.018723 0.050388 0.016402 0.119697 0.161399 0.012776 0.035838 0.057019 0.030913 0.043472 0.049935 0.012600 0.039929 0.133894;
78
79 [ main definition of EX2 with fixed component rates ]
80 model EX2 =MIX{BurEX2:0.672020808818762,ExpEX2:1.6413466609931};
81
82
83 [ ---------------------------------------------------------
84 EX3 mixture model of Le, Lartillot & Gascuel (2008)
85 --------------------------------------------------------- ]
86
87 [ Buried component ]
88 model BurEX3 =
89 0.352598
90 0.216996 1.087422
91 0.292440 0.323465 7.797086
92 2.610812 0.913640 1.460331 0.344397
93 0.510610 5.128748 2.811070 0.773241 0.220223
94 0.753729 1.090823 0.956820 12.012282 0.021022 10.123412
95 2.838061 0.595013 0.884971 0.922298 0.707214 0.351856 0.713974
96 0.239679 3.625577 7.108377 1.826237 0.481109 10.246488 0.839852 0.219310
97 0.051496 0.102940 0.168735 0.024207 0.162795 0.087881 0.036973 0.004515 0.079975
98 0.119849 0.316151 0.091984 0.018800 0.422679 0.648064 0.075035 0.016317 0.282195 2.225363
99 0.443183 20.766910 3.194817 0.568138 0.132784 7.478955 4.176123 0.551523 1.415394 0.163276 0.207613
100 0.460570 0.458210 0.398615 0.059146 0.765112 2.134261 0.313124 0.053192 0.340474 2.609469 4.476961 1.014674
101 0.089411 0.056698 0.104720 0.027913 0.630095 0.094857 0.023275 0.034031 0.691151 0.491179 1.606618 0.077868 1.226530
102 0.993370 0.419898 0.217106 0.273526 0.181230 0.729534 0.311152 0.192454 0.483200 0.040002 0.170402 0.376998 0.075002 0.057218
103 6.108406 1.066008 5.182562 1.216396 5.236005 1.159086 0.763810 2.404073 0.924395 0.048875 0.084247 0.923997 0.260340 0.260617 1.208454
104 1.992855 0.687262 2.181095 0.312299 2.276505 0.829879 0.551397 0.101409 0.480998 0.610331 0.198919 1.407257 1.292634 0.096955 0.648250 8.527249
105 0.063159 0.855332 0.134012 0.099769 0.468450 0.329372 0.136731 0.169991 0.745868 0.056715 0.377293 0.137955 0.463394 2.343596 0.058650 0.211406 0.085948
106 0.078057 0.341493 0.655744 0.241264 0.762740 0.302096 0.142491 0.040257 5.226086 0.092084 0.180292 0.311130 0.249838 8.141649 0.062812 0.267992 0.128044 3.047417
107 1.339724 0.144916 0.125078 0.062854 1.481083 0.194081 0.225389 0.043663 0.090575 5.973306 0.993888 0.222252 0.964622 0.262045 0.207448 0.083450 1.544911 0.078358 0.105286
108
109 0.123992 0.016529 0.017595 0.015784 0.019325 0.015552 0.015939 0.049573 0.014540 0.126555 0.167605 0.011083 0.037438 0.058363 0.028849 0.042324 0.049207 0.011962 0.037833 0.139953;
110
111 [ Intermediate component ]
112 model IntEX3 =
113 0.489239
114 0.466919 0.536794
115 0.601908 0.069474 4.603441
116 2.430552 1.807414 0.997223 0.166431
117 1.101971 2.081359 1.299123 0.508086 0.393348
118 1.227777 0.215899 0.345545 3.579383 0.046861 3.113235
119 1.873072 0.390054 1.528288 0.941969 0.867139 0.349219 0.406414
120 0.519003 1.930915 5.003737 0.781887 1.630085 3.567804 0.324903 0.315383
121 0.158722 0.180317 0.295816 0.013254 0.642786 0.179498 0.090830 0.013181 0.209208
122 0.345026 0.503290 0.138767 0.024393 1.107569 1.027755 0.123806 0.048549 0.592981 5.439892
123 0.610178 4.322929 1.524318 0.121994 0.181609 2.674484 0.792405 0.276766 0.591509 0.301836 0.294950
124 0.949957 0.472702 0.502710 0.091008 1.283305 1.905885 0.242081 0.140301 0.378459 6.259505 9.391081 1.074513
125 0.247271 0.069820 0.161809 0.028611 2.065479 0.077874 0.025753 0.065388 1.541097 1.306479 3.015722 0.048689 2.243101
126 1.334722 0.170174 0.099375 0.211869 0.163190 0.349495 0.155436 0.186099 0.300496 0.065625 0.265961 0.162529 0.088677 0.083754
127 5.316955 0.699036 4.526191 1.143652 5.249370 0.970695 0.438792 2.366185 0.939629 0.138819 0.275119 0.532771 0.521510 0.547761 1.187779
128 1.963809 0.535034 2.034583 0.383040 2.012437 0.891145 0.531018 0.180104 0.467342 1.861944 0.395319 1.071879 2.340268 0.183984 0.400373 7.243848
129 0.145693 0.378596 0.046601 0.048388 1.074147 0.174525 0.063777 0.168836 0.822524 0.110645 0.677913 0.062047 0.796395 3.502387 0.046950 0.290501 0.107097
130 0.195764 0.149382 0.534652 0.105996 2.446201 0.150150 0.071967 0.031908 6.198893 0.299207 0.413150 0.090874 0.492692 15.039152 0.044765 0.328289 0.175204 3.125850
131 2.227504 0.220361 0.150316 0.066496 3.112801 0.393451 0.444469 0.108811 0.224352 15.532696 2.152640 0.302279 2.658339 0.738053 0.322254 0.197018 2.507055 0.175763 0.276642
132
133 0.086346 0.080808 0.041727 0.064440 0.006654 0.052795 0.092110 0.048527 0.028831 0.040497 0.071679 0.079687 0.018007 0.025901 0.052632 0.052778 0.056138 0.010733 0.034744 0.054964;
134
135 [ Highly exposed component ]
136 model HExEX3 =
137 0.557500
138 0.467024 0.508965
139 0.660464 0.044039 3.386724
140 1.332582 3.667491 1.440486 0.185886
141 1.402485 2.156104 1.297398 0.333117 0.789370
142 1.259192 0.111162 0.245837 2.707953 0.058650 2.098300
143 0.934526 0.393780 2.196372 0.868249 1.336358 0.322363 0.252359
144 0.518929 3.157422 5.392488 0.748008 3.827563 4.517669 0.284167 0.634601
145 0.279723 0.407537 0.535113 0.054030 3.345087 0.427624 0.148200 0.015686 0.658979
146 0.715094 1.182387 0.270883 0.035162 3.520931 2.366650 0.172395 0.100089 1.779380 18.830270
147 0.694526 3.728628 1.747648 0.083685 0.100399 2.477205 0.623294 0.280977 0.694965 0.569776 0.493141
148 1.338414 1.261833 0.818216 0.054313 3.918703 2.383718 0.219943 0.228757 0.867786 19.605444 31.431195 1.089056
149 0.295523 0.190129 0.263800 0.044853 5.266468 0.120909 0.042178 0.194665 3.494314 5.825792 11.527190 0.044361 6.237844
150 1.085021 0.168461 0.041147 0.203765 0.185173 0.353420 0.218194 0.120292 0.375260 0.116875 0.705493 0.190747 0.139085 0.108823
151 4.090024 0.852803 4.335615 0.829194 6.499129 1.095446 0.336922 1.733724 1.144100 0.413986 0.878828 0.631498 0.730416 1.167593 1.195720
152 2.318400 0.650016 2.351068 0.385247 1.883085 1.167877 0.532167 0.187062 0.796107 4.825759 0.838744 1.268311 4.445757 0.381760 0.419944 7.677284
153 0.134371 1.021826 0.151293 0.065183 3.716538 0.530580 0.077516 0.396559 1.324147 0.443432 3.290145 0.064651 4.411035 13.056874 0.056705 0.534908 0.408415
154 0.212989 0.424870 1.115762 0.268883 8.874037 0.255572 0.125866 0.107717 14.436023 1.292209 1.491799 0.104026 2.063744 49.760746 0.057618 0.756357 0.396791 12.032322
155 3.112666 0.544010 0.214411 0.125541 5.301703 0.868794 0.839508 0.215758 0.533676 46.074660 7.301056 0.557248 9.151909 2.634769 0.523205 0.564572 4.519860 0.456880 0.670812
156
157 0.094155 0.070537 0.052200 0.112406 0.002213 0.062733 0.165272 0.062302 0.019853 0.011154 0.019829 0.108860 0.006503 0.006873 0.070091 0.057931 0.046183 0.002449 0.008629 0.019827;
158
159 [ main definition of EX3 with fixed component rates ]
160 model EX3 = MIX{BurEX3:0.427672756793791,IntEX3:0.837595938019774,HExEX3:1.51863631431518};
161
162 [ ---------------------------------------------------------
163 EHO mixture model of Le, Lartillot & Gascuel (2008)
164 --------------------------------------------------------- ]
165
166 [ extended component ]
167 model ExtEHO =
168 0.221750
169 0.256487 0.595368
170 0.447755 0.112310 7.769815
171 4.893140 0.929131 1.061884 0.164472
172 0.542660 2.886791 1.927072 0.497273 0.133291
173 0.549459 0.290798 0.518264 5.393249 0.003776 4.326528
174 5.411319 0.302948 0.907713 0.961651 1.249183 0.173873 0.316780
175 0.283752 2.760038 5.159285 0.978418 0.737799 5.086066 0.421812 0.209276
176 0.026683 0.053027 0.166715 0.016491 0.151942 0.055934 0.026726 0.001780 0.098605
177 0.226816 0.251641 0.062256 0.015837 0.763554 0.537705 0.042909 0.032938 0.321607 3.217159
178 0.235513 6.017300 2.543177 0.223507 0.023575 3.432847 1.211039 0.160545 0.671045 0.082221 0.106179
179 0.992834 0.351969 0.415447 0.041511 1.271632 1.700679 0.111984 0.117596 0.326393 3.329162 7.496635 0.519821
180 0.191967 0.041219 0.090517 0.014810 1.004694 0.042779 0.011177 0.040989 0.641267 0.813011 2.233318 0.023173 1.863238
181 1.876507 0.395175 0.362650 0.550534 0.174031 0.731229 0.412907 0.205341 0.381717 0.011597 0.315127 0.393303 0.135360 0.043846
182 6.066032 1.083228 5.612711 1.035540 4.263932 1.429211 0.766802 2.266299 1.074108 0.047896 0.147065 0.683291 0.352118 0.382422 1.462674
183 1.827471 0.645132 1.883173 0.287521 1.395928 1.013709 0.781080 0.055140 0.512000 0.588357 0.142327 1.256445 1.435179 0.079647 0.417388 6.092548
184 0.101419 0.452274 0.065206 0.034173 0.592031 0.164037 0.049674 0.183473 0.741383 0.069289 0.429275 0.050856 0.545447 2.178510 0.022770 0.304839 0.111242
185 0.091914 0.112094 0.451176 0.108762 1.183567 0.132194 0.042952 0.030418 4.373360 0.122828 0.186938 0.096667 0.344096 8.276255 0.053251 0.325231 0.135310 2.597897
186 1.970427 0.119016 0.091863 0.041044 1.750822 0.222903 0.225961 0.053387 0.123318 6.815243 1.427658 0.124284 1.427074 0.341263 0.127045 0.076658 1.052442 0.073165 0.101733
187
188 0.062087 0.053435 0.023743 0.032063 0.013132 0.034151 0.061042 0.030664 0.022696 0.104732 0.099541 0.054991 0.022312 0.045996 0.025392 0.045673 0.072789 0.012691 0.043790 0.139079;
189
190 [ Helix component ]
191 model HelEHO =
192 0.346476
193 0.374362 0.664870
194 0.557349 0.079157 3.710526
195 3.192474 1.027228 0.891196 0.006722
196 0.776545 1.902860 1.561002 0.517360 0.112028
197 0.841893 0.158406 0.443065 3.792847 0.000006 2.320685
198 4.037113 0.661209 1.866962 1.144918 1.465540 0.511489 0.573208
199 0.394225 2.123760 5.845902 0.737868 1.084909 3.960964 0.270146 0.380762
200 0.111350 0.099645 0.233216 0.005627 0.839533 0.089484 0.019520 0.021251 0.132153
201 0.193017 0.307622 0.115495 0.009651 1.136538 0.584189 0.039838 0.048105 0.485901 4.915707
202 0.481682 3.827872 1.926308 0.163314 0.021755 2.487895 0.768919 0.327002 0.534206 0.147053 0.136159
203 0.610432 0.344033 0.452639 0.035659 1.624032 1.146169 0.103241 0.171164 0.364836 6.260678 7.738615 0.549401
204 0.147278 0.035167 0.106276 0.018468 1.864906 0.047207 0.010268 0.086543 1.244539 0.927331 3.243633 0.016265 2.326533
205 1.090575 0.181605 0.093658 0.386490 0.097655 0.462559 0.290152 0.568098 0.458437 0.043237 0.207460 0.198291 0.061027 0.067592
206 6.243684 0.836138 5.633664 0.952131 6.398291 1.267404 0.430602 5.463144 1.088326 0.102127 0.193860 0.707365 0.438507 0.470620 1.534272
207 2.847158 0.566364 2.984732 0.347047 3.711971 1.083181 0.495700 0.500029 0.642773 1.698955 0.402699 1.111399 2.483456 0.231119 0.685164 8.832473
208 0.090983 0.369015 0.085583 0.046821 0.950521 0.183299 0.040785 0.391093 0.950288 0.075780 0.624335 0.041505 0.980672 3.915972 0.053806 0.299723 0.100663
209 0.152848 0.170981 0.594708 0.106099 2.051641 0.121416 0.047614 0.064377 8.167042 0.195540 0.352598 0.069186 0.465779 15.178886 0.058255 0.405459 0.201603 4.035822
210 2.140511 0.136453 0.145376 0.046174 4.011687 0.191618 0.192292 0.202844 0.174981 14.460840 2.175028 0.136317 2.393838 0.659302 0.418505 0.180248 3.585329 0.175143 0.281722
211
212 0.121953 0.076798 0.032215 0.066765 0.006842 0.061304 0.131841 0.026596 0.020392 0.047287 0.087919 0.084679 0.020970 0.024145 0.025871 0.042103 0.038715 0.008346 0.023841 0.051421;
213
214 [ Other component ]
215 model OthEHO =
216 0.529263
217 0.379476 0.612335
218 0.516691 0.067732 4.012914
219 3.774890 1.615176 0.888663 0.165810
220 1.312262 2.913667 1.533683 0.442262 0.337571
221 1.403437 0.154460 0.333334 3.815893 0.015567 3.743866
222 1.272402 0.389317 1.243222 0.661976 0.554904 0.332656 0.319770
223 0.558733 2.816641 4.803000 0.761339 1.223662 4.889028 0.323617 0.300981
224 0.124057 0.155080 0.219635 0.019097 0.560959 0.100743 0.038076 0.005599 0.184752
225 0.340362 0.580087 0.119838 0.015948 1.192857 1.156516 0.083154 0.031031 0.646292 7.873544
226 0.706732 5.734632 1.847806 0.128114 0.050896 3.616626 1.131071 0.283950 0.643558 0.179831 0.224320
227 1.056749 0.665355 0.399943 0.053900 1.893946 2.299714 0.168079 0.085094 0.556024 8.136055 14.213193 0.931689
228 0.233961 0.079465 0.130295 0.016768 1.902244 0.077611 0.012655 0.048906 1.403178 1.581816 4.275863 0.036062 2.888633
229 1.518830 0.252482 0.049484 0.171011 0.108909 0.501196 0.346600 0.058913 0.299924 0.073007 0.297573 0.249478 0.091619 0.068920
230 5.595735 0.861017 3.749627 0.987083 4.952776 1.045071 0.463265 1.190738 0.897478 0.131753 0.265701 0.607097 0.399537 0.408758 0.993614
231 2.157458 0.613623 1.733380 0.361861 2.145775 1.011592 0.523086 0.091023 0.450662 1.492403 0.408418 1.143233 2.378569 0.131777 0.381007 7.574340
232 0.151895 0.544292 0.060182 0.043433 1.259614 0.228038 0.045082 0.134804 0.748147 0.134416 0.979277 0.038787 0.908253 4.850762 0.052415 0.249753 0.114232
233 0.219509 0.243507 0.580103 0.130214 2.325021 0.196580 0.079660 0.037482 6.907609 0.299245 0.552917 0.067894 0.685250 19.404995 0.047839 0.323207 0.183044 4.704884
234 3.049976 0.278740 0.134120 0.055382 4.149385 0.500946 0.435957 0.067170 0.214393 22.435652 2.883298 0.323886 3.369448 0.722571 0.315978 0.152899 2.423398 0.186495 0.303833
235
236 0.076458 0.052393 0.055429 0.088634 0.007473 0.040671 0.080952 0.100192 0.025439 0.031730 0.053100 0.070835 0.014039 0.023159 0.087111 0.063636 0.055346 0.007033 0.023779 0.042590;
237
238 [ main definition of EHO with fixed component rates ]
239 model EHO = MIX{ExtEHO:0.720274356,HelEHO:0.976798797,OthEHO:0.783109376};
240
241
242 [ ---------------------------------------------------------
243 UL2 mixture model of Le, Lartillot & Gascuel (2008)
244 --------------------------------------------------------- ]
245
246 model M1_UL2 =
247 0.267149
248 0.211944 0.816250
249 0.156648 0.336150 3.110967
250 2.402535 1.001114 1.287205 0.467161
251 0.301870 3.168646 1.844180 0.571540 0.394361
252 0.503678 1.529332 0.788530 3.920399 0.234553 8.502278
253 3.124853 0.171548 0.220006 0.250690 0.766651 0.174653 0.399019
254 0.139279 1.597241 5.622886 2.146897 0.349557 8.097306 1.211287 0.044878
255 0.037158 0.139068 0.189483 0.049336 0.147864 0.122799 0.153664 0.006928 0.085276
256 0.108752 0.387538 0.092568 0.035815 0.399254 0.617370 0.225586 0.018972 0.202328 2.343778
257 0.255267 15.176345 1.030178 0.196011 0.396427 3.731061 2.642525 0.142626 0.878376 0.319044 0.422741
258 0.430988 0.522887 0.351960 0.102916 0.683070 2.247889 0.621957 0.070803 0.228871 2.780325 4.767336 1.450453
259 0.088392 0.116382 0.114044 0.066251 0.668683 0.133418 0.075116 0.039034 0.780377 0.488538 1.586897 0.143427 1.211385
260 1.303487 0.178064 0.192016 0.065259 0.315140 0.406966 0.144065 0.135536 0.273070 0.087171 0.298010 0.087701 0.165232 0.104423
261 7.472990 0.579607 3.004054 0.854304 5.789930 0.930019 0.709540 2.018826 0.527351 0.051443 0.070322 0.432286 0.281917 0.286341 0.473611
262 2.276542 0.392852 1.332166 0.193248 2.577504 0.541748 0.690939 0.052900 0.272814 0.634227 0.224553 0.795413 1.360016 0.120449 0.745729 6.088861
263 0.048841 0.673695 0.076107 0.073261 0.377566 0.284556 0.284138 0.130136 0.649073 0.047797 0.324911 0.148403 0.390301 2.189403 0.122493 0.131225 0.080727
264 0.073190 0.425791 0.503951 0.250485 0.577049 0.306036 0.198368 0.024991 3.987606 0.083215 0.127898 0.372637 0.179514 7.784255 0.089874 0.175724 0.117177 2.629196
265 1.351002 0.175990 0.120675 0.105544 1.491339 0.203270 0.463186 0.055506 0.065132 6.411609 1.020423 0.337618 1.047308 0.272790 0.407545 0.079844 1.634833 0.077263 0.083195
266
267 0.122413 0.017757 0.020209 0.012086 0.018894 0.014525 0.009897 0.045663 0.020120 0.124002 0.168915 0.011684 0.037631 0.063612 0.023347 0.039268 0.046707 0.015603 0.050968 0.136701;
268
269
270 model M2_UL2 =
271 0.557363
272 0.539068 0.465628
273 0.696831 0.032997 3.879799
274 1.480953 4.566841 1.777582 0.310752
275 1.402193 1.920868 1.276554 0.327085 0.972350
276 1.335667 0.096752 0.255510 2.685052 0.088385 2.281328
277 1.056193 0.423348 2.171283 0.933450 1.398738 0.369406 0.334900
278 0.729300 2.712485 5.461073 0.679965 5.202985 4.012284 0.282038 0.585359
279 0.267035 0.493033 0.523699 0.023230 2.563394 0.459103 0.176281 0.010013 0.551901
280 0.700687 0.932999 0.206875 0.025161 3.939537 1.918986 0.154733 0.085684 1.446302 8.189198
281 0.736759 3.603558 1.676442 0.070721 0.292188 2.403019 0.611829 0.307607 0.675279 0.627044 0.410941
282 1.505101 0.819561 0.736222 0.089302 4.462071 2.539203 0.250970 0.204790 0.654198 11.105816 15.171688 1.258549
283 0.541573 0.185468 0.343735 0.042217 5.958046 0.156533 0.064557 0.188906 3.891682 3.152154 5.098336 0.088022 4.518197
284 1.155460 0.142408 0.044854 0.175385 0.123605 0.316005 0.157783 0.157894 0.347393 0.047328 0.344717 0.153954 0.054635 0.108793
285 3.823040 0.733964 4.846938 0.890611 7.416660 0.987912 0.343107 2.296896 1.193558 0.368432 0.667347 0.535051 0.754875 1.469714 1.242760
286 1.897039 0.590040 2.371940 0.347041 1.619173 1.025240 0.479587 0.210934 0.728868 5.106169 0.726618 1.152768 3.985684 0.433442 0.358997 9.007029
287 0.296375 0.833840 0.091310 0.080326 5.217767 0.363445 0.078944 0.378088 1.571919 0.351013 2.139511 0.098671 2.796573 6.102504 0.023698 0.665667 0.292919
288 0.297444 0.206563 0.871576 0.173621 11.803422 0.181973 0.110832 0.073892 12.757344 1.161331 1.646025 0.101481 1.732368 29.335598 0.037045 0.706902 0.346859 5.666524
289 2.765737 0.415803 0.194725 0.093474 5.264577 0.734884 0.683342 0.156374 0.517626 26.038986 3.741256 0.457775 5.253478 1.999427 0.297563 0.344932 4.012753 0.385172 0.870088
290
291 0.087622 0.083588 0.048847 0.098882 0.002815 0.062809 0.143166 0.055391 0.023310 0.015495 0.032465 0.102135 0.009511 0.008409 0.069323 0.057733 0.051876 0.003945 0.014462 0.028216;
292
293 model UL2 = MIX{M1_UL2:0.581348617,M2_UL2:1.465482789};
294
295
296 [ ---------------------------------------------------------
297 UL3 mixture model of Le, Lartillot & Gascuel (2008)
298 --------------------------------------------------------- ]
299
300 model Q1_UL3 =
301 0.514865
302 0.774348 0.583403
303 0.854291 0.046141 2.011233
304 1.019817 5.652322 2.260587 0.057603
305 1.095968 1.696154 1.296536 0.417322 0.967032
306 1.054599 0.084924 0.368384 3.592374 0.063073 1.885301
307 3.510012 0.797055 1.759631 1.421695 2.627911 0.743770 0.772359
308 0.694799 2.596186 4.214186 0.654590 6.673533 3.664595 0.294967 0.608220
309 0.344837 0.543739 0.965435 0.062495 2.500862 0.452448 0.155720 0.083334 0.905291
310 0.593987 0.857922 0.351903 0.045358 3.290242 1.421539 0.109100 0.230693 1.595696 5.042430
311 0.708843 2.012940 1.662582 0.106190 0.329149 2.268825 0.579185 0.365374 0.696286 0.701896 0.398546
312 0.990080 0.754111 0.910436 0.143464 3.570847 1.708803 0.181804 0.706982 0.789517 8.138995 13.390024 1.137779
313 0.085639 0.012721 0.098898 0.018361 2.148695 0.012425 0.009316 0.135782 0.921964 1.006572 2.479349 0.014715 1.418875
314 0.655013 0.150052 0.120388 0.698261 0.254951 0.353826 0.250818 0.715043 0.329691 0.170251 0.827093 0.187804 0.178490 0.048299
315 2.863328 0.657706 3.761619 0.619692 9.817007 0.810603 0.344050 6.758412 0.997214 0.414623 0.625678 0.555290 0.647617 0.392859 0.929152
316 1.373936 0.392433 2.711122 0.237865 2.460302 0.701472 0.319136 0.607889 0.728133 3.705396 0.412346 0.953939 2.446017 0.054119 0.279699 9.934970
317 0.247598 0.514750 0.144529 0.157484 5.383077 0.199950 0.045688 0.790171 1.116595 0.243053 1.738186 0.070214 3.427855 3.275850 0.007577 0.583988 0.205721
318 0.090644 0.046952 0.326197 0.089450 7.475195 0.018555 0.020706 0.016617 3.728614 0.404819 0.617948 0.029889 0.956437 47.933104 0.050416 0.181180 0.070113 5.242459
319 2.093798 0.323334 0.307076 0.101486 8.553531 0.473023 0.410909 0.459941 0.568017 13.906640 1.778101 0.426825 2.763369 0.570421 0.311278 0.389524 2.915452 0.252168 0.268516
320
321 0.104307 0.092553 0.043722 0.085643 0.003218 0.074342 0.163928 0.024243 0.022216 0.016012 0.038591 0.105577 0.011434 0.016126 0.018057 0.061232 0.061373 0.004086 0.020876 0.032465;
322
323 model Q2_UL3 =
324 1.709484
325 0.184309 0.860448
326 0.660851 0.182073 4.471383
327 4.554487 2.843438 1.801073 1.068728
328 3.425703 6.092362 2.868388 0.790473 0.794773
329 4.278840 0.359055 0.585031 4.176143 0.121031 6.860012
330 0.625715 1.054231 1.222442 0.492366 1.418419 0.796035 0.643251
331 1.089116 6.396197 8.965630 1.915247 2.033352 11.058341 0.768162 0.523196
332 0.024545 0.023433 0.014686 0.002204 0.628823 0.008720 0.008363 0.002485 0.046726
333 0.150945 0.140520 0.002514 0.000212 1.903535 0.384413 0.015127 0.010251 0.210723 5.066207
334 1.751314 12.981698 3.641808 0.278298 0.036599 7.677610 2.744099 0.612733 1.686490 0.042380 0.023858
335 0.475876 0.364580 0.063143 0.001486 3.890832 0.754732 0.041044 0.024222 0.236955 5.752463 12.019762 0.229898
336 0.142125 0.051255 0.006503 0.000593 5.397699 0.064190 0.006871 0.015588 0.424840 1.005341 5.458275 0.021422 1.779060
337 5.433246 1.051312 0.012611 0.027267 0.635181 1.765792 0.849429 0.023324 0.610884 0.000184 0.037705 0.604166 0.001415 0.003197
338 6.267113 1.750009 5.986041 1.411952 5.482009 1.923966 0.595886 0.943724 1.786620 0.043381 0.066093 0.813893 0.053557 0.199095 1.723045
339 6.389458 1.828974 2.044599 1.561907 2.083626 2.070125 1.210529 0.217976 1.192222 0.515450 0.199809 2.020941 1.238100 0.150760 1.727569 9.882473
340 0.281689 1.180712 0.000006 0.017218 3.696424 0.146508 0.068518 0.222418 0.497727 0.199828 1.849405 0.001429 1.394852 2.473491 0.016401 0.288550 0.190290
341 0.302638 0.475135 0.196905 0.067615 6.355457 0.576342 0.232832 0.059485 4.525509 0.571811 1.194578 0.006674 0.467694 8.107893 0.024556 0.394389 0.441794 4.067825
342 11.333027 0.298555 0.053673 0.009846 5.743238 0.296166 0.413471 0.120393 0.105418 9.130937 2.674960 0.165290 4.417978 1.811161 0.492985 0.042803 3.284174 0.844277 2.327679
343
344 0.044015 0.021591 0.056258 0.102405 0.003260 0.018409 0.041364 0.168549 0.015843 0.064277 0.118096 0.036061 0.027358 0.036695 0.124914 0.047807 0.022696 0.005866 0.018644 0.025892;
345
346
347 model Q3_UL3 =
348 0.063622
349 0.118948 0.528684
350 0.065502 0.142677 12.092355
351 2.010382 0.302352 1.127688 0.014546
352 0.169022 2.026184 1.256016 0.417582 0.170493
353 0.172876 0.453837 0.454428 1.882165 0.045799 4.705997
354 5.254550 0.174422 0.364886 0.192790 0.891120 0.148450 0.195211
355 0.090586 1.258840 5.523808 0.313487 0.211550 4.734918 0.466811 0.096529
356 0.034911 0.065167 0.222440 0.023060 0.132230 0.122571 0.075521 0.003942 0.065261
357 0.146425 0.219004 0.136129 0.028165 0.448432 0.795591 0.146014 0.016718 0.240024 2.387089
358 0.041117 11.082325 0.783756 0.049843 0.039616 1.828161 0.649991 0.069199 0.271006 0.094864 0.140698
359 0.599734 0.230551 0.595641 0.059404 0.699534 2.765355 0.391569 0.089210 0.206188 3.020110 2.806927 0.516762
360 0.148889 0.145244 0.408811 0.089283 0.724422 0.260910 0.101509 0.101882 1.508086 0.693424 0.709933 0.061880 1.887041
361 0.378131 0.225548 0.181924 0.038283 0.146379 0.511097 0.151769 0.166424 0.386101 0.186116 0.753595 0.182723 0.420131 0.341199
362 8.340091 0.495564 3.010756 0.463573 5.601734 0.985082 0.415256 2.532014 0.720035 0.067860 0.121784 0.279698 0.626080 0.788724 0.890779
363 1.932342 0.358779 1.069003 0.093122 2.028674 0.637861 0.597230 0.019551 0.211054 0.870341 0.381670 0.461083 2.131453 0.255120 0.604567 3.450887
364 0.031419 0.378744 0.085588 0.008303 0.277628 0.277906 0.122038 0.055246 0.420382 0.021973 0.127345 0.027776 0.139098 3.077241 0.163299 0.177114 0.062650
365 0.106283 0.366786 1.453278 0.404793 0.753053 0.475024 0.273992 0.055936 7.367304 0.094629 0.126746 0.148716 0.369726 5.251757 0.232549 0.676796 0.247828 2.910495
366 1.104848 0.069287 0.110149 0.084224 1.280832 0.175361 0.342585 0.047507 0.038768 8.415916 1.577573 0.054532 1.537983 0.409619 0.309028 0.094413 1.483411 0.060147 0.076595
367
368 0.134055 0.044392 0.020730 0.020801 0.021008 0.024509 0.028587 0.029069 0.028138 0.105826 0.117458 0.049732 0.026120 0.038984 0.016306 0.038369 0.055334 0.017276 0.039905 0.143398;
369
370 model UL3 = MIX{Q1_UL3:0.484340397,Q2_UL3:0.492780514,Q3_UL3:1.15597274};
371
372
373 [ ---------------------------------------------------------
374 EX_EHO mixture model of Le & Gascuel (2010)
375 --------------------------------------------------------- ]
376
377
378 model BUR_EXT =
379 0.228492
380 0.165543 0.916344
381 0.238509 0.258514 8.498064
382 3.374029 1.037434 1.667702 0.332072
383 0.344742 4.971495 2.471912 0.654950 0.130301
384 0.417921 1.039226 0.875808 13.073209 0.040759 9.834742
385 4.248714 0.411876 0.585570 0.748848 0.908311 0.221633 0.593504
386 0.182762 3.872065 6.999812 1.719470 0.493863 8.695395 0.749303 0.137367
387 0.011705 0.090751 0.149898 0.021996 0.077693 0.043664 0.013820 0.001527 0.073342
388 0.133793 0.286232 0.065118 0.015540 0.456304 0.546974 0.052641 0.024196 0.226460 2.160734
389 0.249141 17.756919 3.385483 0.343780 0.093875 6.677050 2.745017 0.295602 1.481997 0.100576 0.167406
390 0.641194 0.342577 0.427146 0.059345 0.867233 2.306480 0.218260 0.058613 0.358032 2.187901 5.151337 0.750049
391 0.118366 0.068606 0.102572 0.009357 0.633943 0.033356 0.012944 0.024474 0.497973 0.534407 1.581972 0.063281 1.329239
392 1.561052 0.483968 0.385170 0.261437 0.310131 0.913924 0.355871 0.175520 0.512823 0.019789 0.295416 0.348527 0.104569 0.059641
393 5.891807 1.320618 5.737159 1.074011 4.702782 1.389531 0.878480 2.178078 1.111068 0.033343 0.094349 1.035903 0.327901 0.292022 1.344678
394 2.059884 0.976165 2.166428 0.369522 1.951862 0.815145 0.575774 0.060834 0.558388 0.422299 0.153549 1.793263 1.268126 0.085468 0.780914 9.031309
395 0.081683 0.814216 0.057557 0.055146 0.450959 0.191881 0.109420 0.144367 0.651978 0.068649 0.345622 0.169527 0.387902 1.883741 0.023466 0.309129 0.111568
396 0.052650 0.248907 0.570101 0.180267 0.701260 0.253975 0.061388 0.025465 4.206114 0.083799 0.147600 0.226848 0.254720 6.549427 0.027521 0.283138 0.141408 2.561108
397 1.355342 0.137437 0.104597 0.051387 1.203830 0.218892 0.194527 0.031054 0.088935 4.577473 1.003647 0.153722 0.883283 0.242657 0.191295 0.068785 0.990922 0.056276 0.078264
398
399 0.087158 0.015906 0.012970 0.012566 0.020325 0.013301 0.013777 0.039603 0.014597 0.161107 0.147775 0.011033 0.031334 0.064281 0.013322 0.035417 0.048583 0.012672 0.045210 0.199064;
400
401
402 model BUR_HEL =
403 0.317211
404 0.209784 1.120865
405 0.315205 0.301050 7.439896
406 2.214446 0.884449 1.356293 0.110768
407 0.465495 4.319791 2.843187 1.082540 0.215988
408 0.668735 0.901135 0.986572 11.245156 0.009874 7.561773
409 3.614157 0.568883 0.972660 1.036117 0.894733 0.409083 0.780808
410 0.249929 3.138701 7.344935 1.747672 0.379845 9.559763 0.842239 0.146008
411 0.059633 0.103290 0.206475 0.017492 0.286194 0.123433 0.037593 0.010910 0.071273
412 0.096230 0.285199 0.113728 0.015874 0.439724 0.547078 0.063675 0.021607 0.303531 2.097349
413 0.380075 15.783354 2.780107 0.569108 0.093004 6.179905 3.209588 0.413960 1.002075 0.185911 0.185249
414 0.371379 0.411553 0.398602 0.076761 0.727245 1.665645 0.249045 0.068128 0.256194 2.940308 3.649539 0.972247
415 0.075616 0.043519 0.096446 0.041118 0.636688 0.102460 0.039991 0.041269 0.839126 0.376556 1.551814 0.064774 1.173962
416 1.100574 0.385197 0.319458 0.353000 0.112549 0.805706 0.369483 0.482895 0.520098 0.058167 0.144341 0.361488 0.074069 0.057968
417 6.832958 0.955160 5.296628 1.265211 6.144756 1.315182 0.902504 3.903795 0.862633 0.072343 0.080478 0.979654 0.330305 0.328917 1.924898
418 2.223205 0.445571 2.461831 0.299635 2.943208 0.830637 0.621903 0.184055 0.468356 0.911139 0.208091 1.343261 1.515339 0.158763 0.915879 9.298787
419 0.062541 0.806724 0.110928 0.132125 0.414525 0.388313 0.191952 0.271274 0.909529 0.025790 0.343842 0.099137 0.543577 2.467147 0.044938 0.215329 0.087955
420 0.082948 0.329591 0.693402 0.286594 0.866329 0.259566 0.167425 0.049038 6.332054 0.093136 0.177755 0.275998 0.261754 8.344684 0.088981 0.335859 0.137177 3.125017
421 1.390479 0.142986 0.175068 0.106294 1.687293 0.159520 0.297915 0.080925 0.085103 6.414688 0.953785 0.240157 1.097345 0.264988 0.373870 0.144230 2.572837 0.089110 0.115941
422
423 0.158060 0.021566 0.016487 0.014079 0.016937 0.020232 0.023096 0.032822 0.014618 0.114447 0.198900 0.014668 0.042840 0.053434 0.015640 0.037275 0.043095 0.012211 0.036330 0.113263;
424
425 model BUR_OTH =
426 0.406682
427 0.246649 0.848592
428 0.364260 0.198690 4.535840
429 3.292044 0.837291 1.295138 0.420726
430 0.735862 4.205085 2.062501 0.427451 0.259335
431 0.954795 0.673046 0.671062 8.395674 0.048284 8.922739
432 1.958847 0.573207 0.632317 0.572264 0.486274 0.345345 0.650009
433 0.312042 2.699661 4.969855 1.181781 0.551188 7.620453 0.701108 0.195346
434 0.071000 0.127041 0.184028 0.030240 0.180591 0.065984 0.039235 0.005033 0.098525
435 0.142298 0.338853 0.086876 0.026095 0.484427 0.867777 0.087780 0.017129 0.309774 3.477136
436 0.624622 18.390649 2.748646 0.442886 0.238266 6.993941 3.906971 0.652336 1.365814 0.219252 0.288480
437 0.610604 0.581287 0.382156 0.048508 0.963147 2.672887 0.384585 0.051334 0.386066 3.752286 6.858529 1.524446
438 0.124670 0.047666 0.102656 0.031532 0.699124 0.129867 0.004923 0.039185 0.701690 0.643782 2.019473 0.104308 1.568249
439 1.126387 0.321347 0.107738 0.137858 0.150346 0.601413 0.310374 0.073794 0.332910 0.056230 0.208204 0.368816 0.078902 0.062410
440 5.908551 0.834735 3.611589 0.969189 4.765870 0.881934 0.528944 1.439305 0.746876 0.060111 0.114374 0.784754 0.235963 0.219009 0.710100
441 1.856381 0.574277 1.573584 0.223054 2.038789 0.763848 0.461329 0.076195 0.396095 0.701247 0.249302 1.091322 1.282643 0.070553 0.419070 6.616977
442 0.069294 0.654056 0.127255 0.078896 0.517561 0.188732 0.125541 0.104279 0.547504 0.066927 0.454998 0.056498 0.425274 2.668838 0.050943 0.151483 0.062698
443 0.128158 0.354167 0.640140 0.182565 0.793990 0.368725 0.157796 0.037084 4.307140 0.140691 0.241076 0.323966 0.293629 9.711414 0.060323 0.207489 0.111492 2.857446
444 1.982761 0.158227 0.115545 0.051117 2.065903 0.338262 0.258245 0.045770 0.089942 10.113118 1.382024 0.431385 1.456614 0.295718 0.273919 0.066465 1.668063 0.113899 0.144981
445
446 0.102123 0.021199 0.032404 0.032350 0.018985 0.017469 0.017625 0.089270 0.021090 0.083642 0.123866 0.012720 0.029789 0.055399 0.072705 0.061298 0.061705 0.013496 0.039682 0.093184;
447
448 model EXP_EXT=
449 0.464716
450 0.597009 0.420578
451 1.010693 0.048553 5.944290
452 3.915828 2.088244 0.878468 0.236108
453 1.156023 1.882317 1.435926 0.338823 0.482742
454 1.131098 0.127150 0.346338 3.317186 0.061060 2.724696
455 4.638659 0.351041 1.379174 1.216518 1.396050 0.199361 0.353970
456 0.657615 2.215990 4.150252 0.717363 1.853969 3.768864 0.347165 0.313421
457 0.078558 0.127092 0.347281 0.032361 0.605448 0.171553 0.104678 0.010608 0.309418
458 0.516672 0.510585 0.105529 0.039188 1.808273 1.017577 0.112010 0.044661 0.772131 5.693102
459 0.519389 3.571104 1.844049 0.109305 0.103105 2.232749 0.653339 0.195325 0.547017 0.219311 0.253086
460 1.658261 0.640712 0.558751 0.063591 1.694880 2.088441 0.194697 0.291701 0.321392 6.220456 12.392618 0.862547
461 0.426071 0.064894 0.132019 0.034872 2.076573 0.085745 0.026972 0.099963 1.388250 1.765294 3.859637 0.032198 3.134107
462 3.082729 0.250470 0.232578 0.376163 0.290522 0.502379 0.240501 0.302007 0.283950 0.013574 0.606936 0.248475 0.226716 0.058246
463 7.012884 0.866957 5.008997 0.814153 4.758346 1.192080 0.595351 2.514269 0.993487 0.135167 0.349525 0.542021 0.512591 0.744682 1.258172
464 2.037755 0.446367 1.618299 0.203392 1.177421 0.840646 0.583757 0.071515 0.466886 1.503883 0.260405 0.934230 2.245607 0.123552 0.258896 4.504833
465 0.171334 0.385971 0.087717 0.019596 1.015512 0.127027 0.037725 0.217844 0.822780 0.095756 0.777332 0.039952 0.977419 3.217291 0.015240 0.301259 0.102153
466 0.194998 0.091803 0.433021 0.086495 3.074882 0.111578 0.041481 0.048438 4.904785 0.336528 0.411742 0.087476 0.640594 14.126821 0.061656 0.338111 0.129249 2.902137
467 2.811391 0.216605 0.127240 0.061503 2.320268 0.390874 0.450783 0.132513 0.234279 12.181354 2.539512 0.233848 3.363159 0.717467 0.138035 0.159602 1.615372 0.132268 0.186175
468
469 0.043140 0.090761 0.034408 0.052848 0.006370 0.053817 0.107749 0.024812 0.029498 0.049134 0.050167 0.098127 0.013722 0.025841 0.037395 0.056505 0.094326 0.012045 0.039238 0.080099;
470
471 model EXP_HEL =
472 0.434227
473 0.551823 0.569806
474 0.698268 0.056291 3.064314
475 2.026002 2.379205 1.077282 0.016649
476 0.986617 1.606282 1.331570 0.426399 0.409724
477 1.005936 0.120122 0.390888 2.999742 0.021217 1.881156
478 3.221202 0.736168 2.269617 1.272893 1.771711 0.622430 0.656603
479 0.515574 2.032567 5.484997 0.666491 2.985549 3.380526 0.265244 0.557878
480 0.200810 0.241566 0.441585 0.009830 1.541200 0.198621 0.069562 0.043838 0.339616
481 0.328669 0.583849 0.178015 0.022077 2.045404 1.046125 0.089148 0.104708 0.875298 8.628242
482 0.598864 3.090263 1.682415 0.113637 0.207957 2.085253 0.582536 0.376534 0.554395 0.371883 0.290692
483 0.799278 0.528354 0.704087 0.062290 2.303849 1.507620 0.173293 0.356580 0.492228 10.028453 12.162732 0.867109
484 0.256227 0.083117 0.192262 0.030759 4.328951 0.078062 0.022890 0.181917 2.406824 2.014776 4.856941 0.041675 3.521229
485 1.118844 0.147481 0.061969 0.323498 0.171678 0.387521 0.237715 0.641036 0.433529 0.069102 0.359935 0.164055 0.063832 0.126592
486 5.069051 0.749554 5.245486 0.840686 7.114530 1.177802 0.382956 6.139836 1.086779 0.194824 0.424579 0.655759 0.682174 0.753148 1.355810
487 2.949741 0.623328 3.248881 0.406219 3.345739 1.214278 0.538553 0.867954 0.747654 3.316346 0.754081 1.193593 3.516479 0.366653 0.622665 7.975653
488 0.115446 0.394156 0.090971 0.055309 1.947845 0.185912 0.046886 0.451084 1.173014 0.277029 1.078778 0.054622 1.516237 5.813526 0.071865 0.359167 0.106921
489 0.205680 0.197878 0.678775 0.118188 4.183184 0.139485 0.059999 0.051336 10.200670 0.507328 0.721921 0.086974 0.741023 24.191458 0.046460 0.489820 0.247367 4.904042
490 2.494211 0.280293 0.235248 0.083648 5.509932 0.429196 0.409105 0.447130 0.351675 23.404006 3.840750 0.300727 4.126659 1.483049 0.675560 0.336101 4.426709 0.309940 0.588217
491
492 0.115826 0.094038 0.037357 0.085821 0.003363 0.073078 0.167709 0.025416 0.021634 0.024147 0.050238 0.106612 0.013318 0.013330 0.029895 0.044902 0.037901 0.006460 0.018548 0.030407;
493
494 model EXP_OTH =
495 0.603175
496 0.478745 0.562615
497 0.608325 0.056553 3.755571
498 2.371839 2.480665 0.889513 0.170707
499 1.551117 2.685995 1.462350 0.424139 0.669728
500 1.624084 0.129505 0.314826 3.404205 0.049823 3.375473
501 0.987777 0.356744 1.294077 0.640234 0.583980 0.331879 0.304731
502 0.667236 2.788429 4.719171 0.731257 1.872668 4.612209 0.316233 0.320454
503 0.186911 0.269245 0.318538 0.028464 0.987958 0.242926 0.090427 0.007312 0.327205
504 0.527992 0.844027 0.167295 0.021423 1.623589 1.636879 0.135662 0.044560 0.939347 10.338048
505 0.842575 5.076266 1.736167 0.106076 0.132985 3.365869 0.969736 0.270931 0.669196 0.356829 0.352830
506 1.296147 0.863599 0.469732 0.075018 1.832599 2.642602 0.217378 0.107935 0.624941 10.670411 17.593544 1.247987
507 0.325034 0.135328 0.192352 0.021631 2.731423 0.103263 0.027708 0.060740 2.148472 2.344767 5.497995 0.057563 3.278627
508 1.670091 0.235642 0.042844 0.164518 0.112539 0.479958 0.326780 0.057540 0.291899 0.110067 0.380466 0.240061 0.109541 0.083760
509 5.098150 0.831455 3.661924 0.978777 4.500240 1.064732 0.455496 1.095629 0.915898 0.226713 0.405000 0.608323 0.525496 0.593321 1.035726
510 2.174502 0.630453 1.791747 0.396219 1.681712 1.083797 0.556968 0.100584 0.457070 2.361119 0.543612 1.211816 2.987220 0.198957 0.368383 7.505908
511 0.203719 0.615713 0.044203 0.046952 1.745090 0.303876 0.050920 0.155176 0.920001 0.165182 1.385828 0.055323 1.274920 5.896599 0.059081 0.303111 0.156402
512 0.271220 0.253084 0.643377 0.142691 3.763228 0.209729 0.093004 0.035856 8.167503 0.490579 0.894778 0.077103 1.029700 26.210400 0.045876 0.373529 0.218567 5.726440
513 3.470639 0.410713 0.180011 0.081584 4.323431 0.751254 0.686467 0.086874 0.318032 29.800262 3.856040 0.482930 4.862267 1.182403 0.390522 0.268937 2.836818 0.229423 0.453335
514
515 0.071716 0.058979 0.060316 0.101089 0.005039 0.044673 0.093349 0.105394 0.026228 0.020220 0.037831 0.081647 0.010677 0.015875 0.090566 0.065046 0.054453 0.005546 0.019924 0.031432;
516
517
518 model EX_EHO = MIX{BUR_EXT:0.761816796788931,BUR_HEL:0.744425646802117,BUR_OTH:0.532457759429489,EXP_EXT:1.5639387472863,EXP_HEL:2.06403411829438,EXP_OTH:1.43336795177594};
519
520
521 [ ---------------------------------------------------------
522 LG4M mixture model of Le, Dang & Gascuel (2012)
523 --------------------------------------------------------- ]
524
525 model LG4M1 =
526 0.269343
527 0.254612 0.150988
528 0.236821 0.031863 0.659648
529 2.506547 0.938594 0.975736 0.175533
530 0.359080 0.348288 0.697708 0.086573 0.095967
531 0.304674 0.156000 0.377704 0.449140 0.064706 4.342595
532 1.692015 0.286638 0.565095 0.380358 0.617945 0.202058 0.264342
533 0.251974 0.921633 1.267609 0.309692 0.390429 2.344059 0.217750 0.104842
534 1.085220 0.325624 0.818658 0.037814 1.144150 0.534567 0.222793 0.062682 0.567431
535 0.676353 0.602366 0.217027 0.007533 1.595775 0.671143 0.158424 0.070463 0.764255 8.226528
536 0.179155 0.971338 1.343718 0.133744 0.122468 0.983857 0.994128 0.220916 0.410581 0.387487 0.181110
537 1.636817 0.515217 0.670461 0.071252 1.534848 5.288642 0.255628 0.094198 0.257229 25.667158 6.819689 1.591212
538 0.235498 0.123932 0.099793 0.030425 0.897279 0.112229 0.022529 0.047488 0.762914 1.344259 0.865691 0.038921 2.030833
539 1.265605 0.040163 0.173354 0.027579 0.259961 0.580374 0.088041 0.145595 0.143676 0.298859 1.020117 0.000714 0.190019 0.093964
540 5.368405 0.470952 5.267140 0.780505 4.986071 0.890554 0.377949 1.755515 0.786352 0.527246 0.667783 0.659948 0.731921 0.837669 1.355630
541 1.539394 0.326789 1.688169 0.283738 1.389282 0.329821 0.231770 0.117017 0.449977 3.531600 0.721586 0.497588 2.691697 0.152088 0.698040 16.321298
542 0.140944 0.375611 0.025163 0.002757 0.801456 0.257253 0.103678 0.132995 0.345834 0.377156 0.839647 0.176970 0.505682 1.670170 0.091298 0.210096 0.013165
543 0.199836 0.146857 0.806275 0.234246 1.436970 0.319669 0.010076 0.036859 3.503317 0.598632 0.738969 0.154436 0.579000 4.245524 0.074524 0.454195 0.232913 1.178490
544 9.435529 0.285934 0.395670 0.130890 6.097263 0.516259 0.503665 0.222960 0.149143 13.666175 2.988174 0.162725 5.973826 0.843416 0.597394 0.701149 4.680002 0.300085 0.416262
545
546 0.082276 0.055172 0.043853 0.053484 0.018957 0.028152 0.046679 0.157817 0.033297 0.028284 0.054284 0.025275 0.023665 0.041874 0.063071 0.066501 0.065424 0.023837 0.038633 0.049465;
547
548 model LG4M2 =
549 0.133720
550 0.337212 0.749052
551 0.110918 0.105087 4.773487
552 3.993460 0.188305 1.590332 0.304942
553 0.412075 2.585774 1.906884 0.438367 0.242076
554 0.435295 0.198278 0.296366 7.470333 0.008443 3.295515
555 7.837540 0.164607 0.431724 0.153850 1.799716 0.269744 0.242866
556 0.203872 2.130334 9.374479 1.080878 0.152458 12.299133 0.279589 0.089714
557 0.039718 0.024553 0.135254 0.014979 0.147498 0.033964 0.005585 0.007248 0.022746
558 0.075784 0.080091 0.084971 0.014128 0.308347 0.500836 0.022833 0.022999 0.161270 1.511682
559 0.177662 10.373708 1.036721 0.038303 0.043030 2.181033 0.321165 0.103050 0.459502 0.021215 0.078395
560 0.420784 0.192765 0.329545 0.008331 0.883142 1.403324 0.168673 0.160728 0.612573 1.520889 7.763266 0.307903
561 0.071268 0.019652 0.088753 0.013547 0.566609 0.071878 0.020050 0.041022 0.625361 0.382806 1.763059 0.044644 1.551911
562 0.959127 1.496585 0.377794 0.332010 0.318192 1.386970 0.915904 0.224255 2.611479 0.029351 0.068250 1.542356 0.047525 0.182715
563 11.721512 0.359408 2.399158 0.219464 9.104192 0.767563 0.235229 3.621219 0.971955 0.033780 0.043035 0.236929 0.319964 0.124977 0.840651
564 2.847068 0.218463 1.855386 0.109808 4.347048 0.765848 0.164569 0.312024 0.231569 0.356327 0.159597 0.403210 1.135162 0.106903 0.269190 9.816481
565 0.030203 0.387292 0.118878 0.067287 0.190240 0.122113 0.007023 0.137411 0.585141 0.020634 0.228824 0.000122 0.474862 3.135128 0.030313 0.093830 0.119152
566 0.067183 0.130101 0.348730 0.061798 0.301198 0.095382 0.095764 0.044628 2.107384 0.046105 0.100117 0.017073 0.192383 8.367641 0.000937 0.137416 0.044722 4.179782
567 0.679398 0.041567 0.092408 0.023701 1.271187 0.115566 0.055277 0.086988 0.060779 8.235167 0.609420 0.061764 0.581962 0.184187 0.080246 0.098033 1.438350 0.023439 0.039124
568
569 0.120900 0.036460 0.026510 0.040410 0.015980 0.021132 0.025191 0.036369 0.015884 0.111029 0.162852 0.024820 0.028023 0.074058 0.012065 0.041963 0.039072 0.012666 0.040478 0.114138;
570
571 model LG4M3 =
572 0.421017
573 0.316236 0.693340
574 0.285984 0.059926 6.158219
575 4.034031 1.357707 0.708088 0.063669
576 0.886972 2.791622 1.701830 0.484347 0.414286
577 0.760525 0.233051 0.378723 4.032667 0.081977 4.940411
578 0.754103 0.402894 2.227443 1.102689 0.416576 0.459376 0.508409
579 0.571422 2.319453 5.579973 0.885376 1.439275 4.101979 0.576745 0.428799
580 0.162152 0.085229 0.095692 0.006129 0.490937 0.104843 0.045514 0.004705 0.098934
581 0.308006 0.287051 0.056994 0.007102 0.958988 0.578990 0.067119 0.024403 0.342983 3.805528
582 0.390161 7.663209 1.663641 0.105129 0.135029 3.364474 0.652618 0.457702 0.823674 0.129858 0.145630
583 1.042298 0.364551 0.293222 0.037983 1.486520 1.681752 0.192414 0.070498 0.222626 4.529623 4.781730 0.665308
584 0.362476 0.073439 0.129245 0.020078 1.992483 0.114549 0.023272 0.064490 1.491794 1.113437 2.132006 0.041677 1.928654
585 1.755491 0.087050 0.099325 0.163817 0.242851 0.322939 0.062943 0.198698 0.192904 0.062948 0.180283 0.059655 0.129323 0.065778
586 3.975060 0.893398 5.496314 1.397313 3.575120 1.385297 0.576191 1.733288 1.021255 0.065131 0.129115 0.600308 0.387276 0.446001 1.298493
587 2.565079 0.534056 2.143993 0.411388 2.279084 0.893006 0.528209 0.135731 0.518741 0.972662 0.280700 0.890086 1.828755 0.189028 0.563778 7.788147
588 0.283631 0.497926 0.075454 0.043794 1.335322 0.308605 0.140137 0.150797 1.409726 0.119868 0.818331 0.080591 1.066017 3.754687 0.073415 0.435046 0.197272
589 0.242513 0.199157 0.472207 0.085937 2.039787 0.262751 0.084578 0.032247 7.762326 0.153966 0.299828 0.117255 0.438215 14.506235 0.089180 0.352766 0.215417 5.054245
590 2.795818 0.107130 0.060909 0.029724 2.986426 0.197267 0.196977 0.044327 0.116751 7.144311 1.848622 0.118020 1.999696 0.705747 0.272763 0.096935 1.820982 0.217007 0.172975
591
592 0.072639 0.051691 0.038642 0.055580 0.009829 0.031374 0.048731 0.065283 0.023791 0.086640 0.120847 0.052177 0.026728 0.032589 0.039238 0.046748 0.053361 0.008024 0.037426 0.098662;
593
594 model LG4M4 =
595 0.576160
596 0.567606 0.498643
597 0.824359 0.050698 3.301401
598 0.822724 4.529235 1.291808 0.101930
599 1.254238 2.169809 1.427980 0.449474 0.868679
600 1.218615 0.154502 0.411471 3.172277 0.050239 2.138661
601 1.803443 0.604673 2.125496 1.276384 1.598679 0.502653 0.479490
602 0.516862 2.874265 4.845769 0.719673 3.825677 4.040275 0.292773 0.596643
603 0.180898 0.444586 0.550969 0.023542 2.349573 0.370160 0.142187 0.016618 0.500788
604 0.452099 0.866322 0.201033 0.026731 2.813990 1.645178 0.135556 0.072152 1.168817 5.696116
605 0.664186 2.902886 2.101971 0.127988 0.200218 2.505933 0.759509 0.333569 0.623100 0.547454 0.363656
606 0.864415 0.835049 0.632649 0.079201 2.105931 1.633544 0.216462 0.252419 0.665406 7.994105 11.751178 1.096842
607 0.324478 0.208947 0.280339 0.041683 4.788477 0.107022 0.067711 0.171320 3.324779 2.965328 5.133843 0.084856 4.042591
608 1.073043 0.173826 0.041985 0.270336 0.121299 0.351384 0.228565 0.225318 0.376089 0.058027 0.390354 0.214230 0.058954 0.126299
609 3.837562 0.884342 4.571911 0.942751 6.592827 1.080063 0.465397 3.137614 1.119667 0.362516 0.602355 0.716940 0.506796 1.444484 1.432558
610 2.106026 0.750016 2.323325 0.335915 1.654673 1.194017 0.617231 0.318671 0.801030 4.455842 0.580191 1.384210 3.522468 0.473128 0.432718 5.716300
611 0.163720 0.818102 0.072322 0.068275 3.305436 0.373790 0.054323 0.476587 1.100360 0.392946 1.703323 0.085720 1.725516 5.436253 0.053108 0.498594 0.231832
612 0.241167 0.302440 1.055095 0.246940 9.741942 0.249895 0.129973 0.052363 11.542498 1.047449 1.319667 0.139770 1.330225 26.562270 0.046986 0.737653 0.313460 5.165098
613 1.824586 0.435795 0.179086 0.091739 3.609570 0.649507 0.656681 0.225234 0.473437 19.897252 3.001995 0.452926 3.929598 1.692159 0.370204 0.373501 3.329822 0.326593 0.860743
614
615 0.104843 0.078835 0.043513 0.090498 0.002924 0.066163 0.151640 0.038843 0.022556 0.018383 0.038687 0.104462 0.010166 0.009089 0.066950 0.053667 0.049486 0.004409 0.012924 0.031962;
616
617 model LG4M = MIX{LG4M1,LG4M2,LG4M3,LG4M4}*G4;
618 model LG4 = MIX{LG4M1,LG4M2,LG4M3,LG4M4}*G4;
619
620
621 [ ---------------------------------------------------------
622 LG4X mixture model of Le, Dang & Gascuel (2012)
623 --------------------------------------------------------- ]
624
625 model LG4X1 =
626 0.295719
627 0.067388 0.448317
628 0.253712 0.457483 2.358429
629 1.029289 0.576016 0.251987 0.189008
630 0.107964 1.741924 0.216561 0.599450 0.029955
631 0.514644 0.736017 0.503084 109.901504 0.084794 4.117654
632 10.868848 0.704334 0.435271 1.070052 1.862626 0.246260 1.202023
633 0.380498 5.658311 4.873453 5.229858 0.553477 6.508329 1.634845 0.404968
634 0.084223 0.123387 0.090748 0.052764 0.151733 0.054187 0.060194 0.048984 0.204296
635 0.086976 0.221777 0.033310 0.021407 0.230320 0.195703 0.069359 0.069963 0.504221 1.495537
636 0.188789 93.433377 0.746537 0.621146 0.096955 1.669092 2.448827 0.256662 1.991533 0.091940 0.122332
637 0.286389 0.382175 0.128905 0.081091 0.352526 0.810168 0.232297 0.228519 0.655465 1.994320 3.256485 0.457430
638 0.155567 0.235965 0.127321 0.205164 0.590018 0.066081 0.064822 0.241077 6.799829 0.754940 2.261319 0.163849 1.559944
639 1.671061 6.535048 0.904011 5.164456 0.386853 2.437439 3.537387 4.320442 11.291065 0.170343 0.848067 5.260446 0.426508 0.438856
640 2.132922 0.525521 0.939733 0.747330 1.559564 0.165666 0.435384 3.656545 0.961142 0.050315 0.064441 0.360946 0.132547 0.306683 4.586081
641 0.529591 0.303537 0.435450 0.308078 0.606648 0.106333 0.290413 0.290216 0.448965 0.372166 0.102493 0.389413 0.498634 0.109129 2.099355 3.634276
642 0.115551 0.641259 0.046646 0.260889 0.587531 0.093417 0.280695 0.307466 6.227274 0.206332 0.459041 0.033291 0.559069 18.392863 0.411347 0.101797 0.034710
643 0.102453 0.289466 0.262076 0.185083 0.592318 0.035149 0.105999 0.096556 20.304886 0.097050 0.133091 0.115301 0.264728 66.647302 0.476350 0.148995 0.063603 20.561407
644 0.916683 0.102065 0.043986 0.080708 0.885230 0.072549 0.206603 0.306067 0.205944 5.381403 0.561215 0.112593 0.693307 0.400021 0.584622 0.089177 0.755865 0.133790 0.154902
645
646 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931;
647
648 model LG4X2 =
649 0.066142
650 0.590377 0.468325
651 0.069930 0.013688 2.851667
652 9.850951 0.302287 3.932151 0.146882
653 1.101363 1.353957 8.159169 0.249672 0.582670
654 0.150375 0.028386 0.219934 0.560142 0.005035 3.054085
655 0.568586 0.037750 0.421974 0.046719 0.275844 0.129551 0.037250
656 0.051668 0.262130 2.468752 0.106259 0.098208 4.210126 0.029788 0.013513
657 0.127170 0.016923 0.344765 0.003656 0.445038 0.165753 0.008541 0.002533 0.031779
658 0.292429 0.064289 0.210724 0.004200 1.217010 1.088704 0.014768 0.005848 0.064558 7.278994
659 0.071458 0.855973 1.172204 0.014189 0.033969 1.889645 0.125869 0.031390 0.065585 0.029917 0.042762
660 1.218562 0.079621 0.763553 0.009876 1.988516 3.344809 0.056702 0.021612 0.079927 7.918203 14.799537 0.259400
661 0.075144 0.011169 0.082464 0.002656 0.681161 0.111063 0.004186 0.004854 0.095591 0.450964 1.506485 0.009457 1.375871
662 7.169085 0.161937 0.726566 0.040244 0.825960 2.067758 0.110993 0.129497 0.196886 0.169797 0.637893 0.090576 0.457399 0.143327
663 30.139501 0.276530 11.149790 0.267322 18.762977 3.547017 0.201148 0.976631 0.408834 0.104288 0.123793 0.292108 0.598048 0.328689 3.478333
664 13.461692 0.161053 4.782635 0.053740 11.949233 2.466507 0.139705 0.053397 0.126088 1.578530 0.641351 0.297913 4.418398 0.125011 2.984862 13.974326
665 0.021372 0.081472 0.058046 0.006597 0.286794 0.188236 0.009201 0.019475 0.037226 0.015909 0.154810 0.017172 0.239749 0.562720 0.061299 0.154326 0.060703
666 0.045779 0.036742 0.498072 0.027639 0.534219 0.203493 0.012095 0.004964 0.452302 0.094365 0.140750 0.021976 0.168432 1.414883 0.077470 0.224675 0.123480 0.447011
667 4.270235 0.030342 0.258487 0.012745 4.336817 0.281953 0.043812 0.015539 0.016212 16.179952 3.416059 0.032578 2.950318 0.227807 1.050562 0.112000 5.294490 0.033381 0.045528
668
669 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372;
670
671 model LG4X3 =
672 0.733336
673 0.558955 0.597671
674 0.503360 0.058964 5.581680
675 4.149599 2.863355 1.279881 0.225860
676 1.415369 2.872594 1.335650 0.434096 1.043232
677 1.367574 0.258365 0.397108 2.292917 0.209978 4.534772
678 1.263002 0.366868 1.840061 1.024707 0.823594 0.377181 0.496780
679 0.994098 2.578946 5.739035 0.821921 3.039380 4.877840 0.532488 0.398817
680 0.517204 0.358350 0.284730 0.027824 1.463390 0.370939 0.232460 0.008940 0.349195
681 0.775054 0.672023 0.109781 0.021443 1.983693 1.298542 0.169219 0.043707 0.838324 5.102837
682 0.763094 5.349861 1.612642 0.088850 0.397640 3.509873 0.755219 0.436013 0.888693 0.561690 0.401070
683 1.890137 0.691594 0.466979 0.060820 2.831098 2.646440 0.379926 0.087640 0.488389 7.010411 8.929538 1.357738
684 0.540460 0.063347 0.141582 0.018288 4.102068 0.087872 0.020447 0.064863 1.385133 3.054968 5.525874 0.043394 3.135353
685 0.200122 0.032875 0.019509 0.042687 0.059723 0.072299 0.023282 0.036426 0.050226 0.039318 0.067505 0.023126 0.012695 0.015631
686 4.972745 0.821562 4.670980 1.199607 5.901348 1.139018 0.503875 1.673207 0.962470 0.204155 0.273372 0.567639 0.570771 0.458799 0.233109
687 1.825593 0.580847 1.967383 0.420710 2.034980 0.864479 0.577513 0.124068 0.502294 2.653232 0.437116 1.048288 2.319555 0.151684 0.077004 8.113282
688 0.450842 0.661866 0.088064 0.037642 2.600668 0.390688 0.109318 0.218118 1.065585 0.564368 1.927515 0.120994 1.856122 4.154750 0.011074 0.377578 0.222293
689 0.526135 0.265730 0.581928 0.141233 5.413080 0.322761 0.153776 0.039217 8.351808 0.854294 0.940458 0.180650 0.975427 11.429924 0.026268 0.429221 0.273138 4.731579
690 3.839269 0.395134 0.145401 0.090101 4.193725 0.625409 0.696533 0.104335 0.377304 15.559906 2.508169 0.449074 3.404087 1.457957 0.052132 0.260296 2.903836 0.564762 0.681215
691
692 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050761;
693
694 model LG4X4 =
695 0.658412
696 0.566269 0.540749
697 0.854111 0.058015 3.060574
698 0.884454 5.851132 1.279257 0.160296
699 1.309554 2.294145 1.438430 0.482619 0.992259
700 1.272639 0.182966 0.431464 2.992763 0.086318 2.130054
701 1.874713 0.684164 2.075952 1.296206 2.149634 0.571406 0.507160
702 0.552007 3.192521 4.840271 0.841829 5.103188 4.137385 0.351381 0.679853
703 0.227683 0.528161 0.644656 0.031467 3.775817 0.437589 0.189152 0.025780 0.665865
704 0.581512 1.128882 0.266076 0.048542 3.954021 2.071689 0.217780 0.082005 1.266791 8.904999
705 0.695190 3.010922 2.084975 0.132774 0.190734 2.498630 0.767361 0.326441 0.680174 0.652629 0.440178
706 0.967985 1.012866 0.720060 0.133055 1.776095 1.763546 0.278392 0.343977 0.717301 10.091413 14.013035 1.082703
707 0.344015 0.227296 0.291854 0.056045 4.495841 0.116381 0.092075 0.195877 4.001286 2.671718 5.069337 0.091278 4.643214
708 0.978992 0.156635 0.028961 0.209188 0.264277 0.296578 0.177263 0.217424 0.362942 0.086367 0.539010 0.172734 0.121821 0.161015
709 3.427163 0.878405 4.071574 0.925172 7.063879 1.033710 0.451893 3.057583 1.189259 0.359932 0.742569 0.693405 0.584083 1.531223 1.287474
710 2.333253 0.802754 2.258357 0.360522 2.221150 1.283423 0.653836 0.377558 0.964545 4.797423 0.780580 1.422571 4.216178 0.599244 0.444362 5.231362
711 0.154701 0.830884 0.073037 0.094591 3.017954 0.312579 0.074620 0.401252 1.350568 0.336801 1.331875 0.068958 1.677263 5.832025 0.076328 0.548763 0.208791
712 0.221089 0.431617 1.238426 0.313945 8.558815 0.305772 0.181992 0.072258 12.869737 1.021885 1.531589 0.163829 1.575754 33.873091 0.079916 0.831890 0.307846 5.910440
713 2.088785 0.456530 0.199728 0.118104 4.310199 0.681277 0.752277 0.241015 0.531100 23.029406 4.414850 0.481711 5.046403 1.914768 0.466823 0.382271 3.717971 0.282540 0.964421
714
715 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010087 0.027158;
716
717 model LG4X = MIX{LG4X1,LG4X2,LG4X3,LG4X4}*R4;
718
719 [ ---------------------------------------------------------
720 +cF class frequency mixture model of Wang et al. (2008)
721 --------------------------------------------------------- ]
722
723 frequency Fclass1 = 0.02549352 0.01296012 0.005545202 0.006005566 0.01002193 0.01112289 0.008811948 0.001796161 0.004312188 0.2108274 0.2730413 0.01335451 0.07862202 0.03859909 0.005058205 0.008209453 0.03210019 0.002668138 0.01379098 0.2376598;
724 frequency Fclass2 = 0.09596966 0.008786096 0.02805857 0.01880183 0.005026264 0.006454635 0.01582725 0.7215719 0.003379354 0.002257725 0.003013483 0.01343441 0.001511657 0.002107865 0.006751404 0.04798539 0.01141559 0.000523736 0.002188483 0.004934972;
725 frequency Fclass3 = 0.01726065 0.005467988 0.01092937 0.3627871 0.001046402 0.01984758 0.5149206 0.004145081 0.002563289 0.002955213 0.005286931 0.01558693 0.002693098 0.002075771 0.003006167 0.01263069 0.01082144 0.000253451 0.001144787 0.004573568;
726 frequency Fclass4 = 0.1263139 0.09564027 0.07050061 0.03316681 0.02095119 0.05473468 0.02790523 0.009007538 0.03441334 0.005855319 0.008061884 0.1078084 0.009019514 0.05018693 0.07948 0.09447839 0.09258897 0.01390669 0.05367769 0.01230413;
727 model CF4 = POISSON+FMIX{Fclass1,Fclass2,Fclass3,Fclass4}+F+G;
728 model JTTCF4G = JTT+FMIX{empirical,Fclass1,Fclass2,Fclass3,Fclass4}+G;
729
730 [ ---------------------------------------------------------
731 CAT-C10 profile mixture model of Le, Gascuel & Lartillot (2008)
732 --------------------------------------------------------- ]
733
734 frequency C10pi1 = 0.4082573125 0.0081783015 0.0096285438 0.0069870889 0.0349388179 0.0075279735 0.0097846653 0.1221613215 0.0039151830 0.0125784287 0.0158338663 0.0059670150 0.0081313216 0.0061604332 0.0394155867 0.1682450664 0.0658132542 0.0018751587 0.0041579747 0.0604426865;
735 frequency C10pi2 = 0.1027763487 0.0418664491 0.0213272051 0.0155943616 0.0149663448 0.0440685478 0.0419667447 0.0138805792 0.0158864807 0.1066076641 0.1131944125 0.0436343681 0.0437800327 0.0180729309 0.0223250701 0.0529608087 0.1081741005 0.0045147205 0.0137373857 0.1606654446;
736 frequency C10pi3 = 0.0351766018 0.0019678632 0.0016591476 0.0006768741 0.0078706538 0.0016559557 0.0019686768 0.0022420602 0.0012878339 0.3515819591 0.1278183107 0.0018856550 0.0242631753 0.0126221329 0.0029771559 0.0049998099 0.0255378034 0.0011907778 0.0037539283 0.3888636245;
737 frequency C10pi4 = 0.0408513927 0.0269887074 0.2185648186 0.2333814790 0.0037602852 0.0380451418 0.0901238869 0.1158332065 0.0373197176 0.0025523644 0.0052164616 0.0485017266 0.0022571778 0.0025108218 0.0108333610 0.0804527209 0.0302879995 0.0010815260 0.0069890931 0.0044481118;
738 frequency C10pi5 = 0.0185492661 0.0062362395 0.0024895723 0.0009775062 0.0070416514 0.0083539447 0.0024891617 0.0028952913 0.0040103982 0.1632422345 0.4443079409 0.0043570878 0.1202815687 0.0733329781 0.0048827648 0.0051642443 0.0131806647 0.0068759784 0.0144734420 0.0968580644;
739 frequency C10pi6 = 0.1106750119 0.0352190043 0.0405186210 0.1636437899 0.0014834855 0.0877962201 0.2638456592 0.0325228293 0.0163803600 0.0068334902 0.0140679579 0.0677158208 0.0048988133 0.0023256777 0.0298982139 0.0562887953 0.0426922497 0.0010338979 0.0040522304 0.0181078719;
740 frequency C10pi7 = 0.0522657662 0.0668294648 0.0714836849 0.0297745257 0.0143324928 0.0736540298 0.0388386669 0.0228101108 0.1551638111 0.0187406149 0.0653779932 0.0439469345 0.0207189121 0.0624033021 0.0145475497 0.0549017631 0.0370140058 0.0193756900 0.1110694548 0.0267512268;
741 frequency C10pi8 = 0.0116587342 0.0050990142 0.0064011054 0.0021742457 0.0105340743 0.0040203734 0.0024251112 0.0034709143 0.0366787049 0.0187185330 0.0676489746 0.0026694717 0.0143534813 0.3650985596 0.0031159927 0.0094848536 0.0073713920 0.0509564551 0.3574858593 0.0206341497;
742 frequency C10pi9 = 0.0627195947 0.2038782162 0.0428629162 0.0236193294 0.0052662886 0.1098111767 0.0686284994 0.0256174957 0.0332612124 0.0128968249 0.0305627740 0.2270839355 0.0124036991 0.0039181841 0.0140440613 0.0483152469 0.0463378087 0.0025143473 0.0065521118 0.0197062770;
743 frequency C10pi10 = 0.1145518598 0.0324008908 0.0750614981 0.0416192189 0.0098549497 0.0339624663 0.0364907910 0.0503817581 0.0165233329 0.0092949460 0.0139153707 0.0423026886 0.0082240805 0.0046605982 0.0379221548 0.2610647896 0.1845829279 0.0017548981 0.0058538316 0.0195769483;
744 model C10 = POISSON+G+FMIX{C10pi1:1:0.1191344178,C10pi2:1:0.0874372456,C10pi3:1:0.1037105070,C10pi4:1:0.0922584809,C10pi5:1:0.1070492801,C10pi6:1:0.1329945166,C10pi7:1:0.0538028458,C10pi8:1:0.0691986212,C10pi9:1:0.1319937434,C10pi10:1:0.1024203429};
745 model C10Opt = POISSON+G+FMIX{C10pi1,C10pi2,C10pi3,C10pi4,C10pi5,C10pi6,C10pi7,C10pi8,C10pi9,C10pi10};
746
747 [ ---------------------------------------------------------
748 CAT-C20 profile mixture model of Le, Gascuel & Lartillot (2008)
749 --------------------------------------------------------- ]
750 frequency C20pi1 = 0.0862412505 0.0171943793 0.0791293376 0.0329908619 0.0130504558 0.0169046938 0.0184526503 0.0366905299 0.0108013340 0.0097907148 0.0112826424 0.0220195221 0.0087821483 0.0044155335 0.0189273201 0.3178152357 0.2711700523 0.0015317305 0.0048342853 0.0179753220 ;
751 frequency C20pi2 = 0.2035582865 0.0050980810 0.0077052407 0.0031656079 0.0348667285 0.0064044073 0.0070859400 0.0195235515 0.0024392035 0.1152573291 0.0789777393 0.0042380850 0.0309187017 0.0112429356 0.0164189221 0.0496777139 0.1118946615 0.0017762569 0.0048448213 0.2849057867 ;
752 frequency C20pi3 = 0.0211547413 0.0014946177 0.0012755030 0.0005492865 0.0048188557 0.0012328812 0.0014539632 0.0011430874 0.0011346394 0.3928460626 0.1250644210 0.0013579946 0.0209788805 0.0128251737 0.0020247248 0.0026240726 0.0171914121 0.0011591071 0.0036027969 0.3860677787 ;
753 frequency C20pi4 = 0.0376903543 0.2885196153 0.0365411474 0.0109469400 0.0064073829 0.0893564381 0.0358365464 0.0191106776 0.0329513951 0.0101711878 0.0237495504 0.2897626974 0.0096528870 0.0036349802 0.0105337370 0.0356313768 0.0355926500 0.0027925238 0.0066557222 0.0144621902 ;
754 frequency C20pi5 = 0.0084597802 0.0053589922 0.0072525884 0.0024487852 0.0084909000 0.0042781483 0.0025055486 0.0024277107 0.0433214027 0.0097713028 0.0380507037 0.0026741007 0.0080724771 0.3420463838 0.0021418673 0.0080418935 0.0055322116 0.0494840193 0.4375001561 0.0121410277 ;
755 frequency C20pi6 = 0.1759898886 0.0290429175 0.0332845569 0.1301263816 0.0017558693 0.0707183953 0.2182166681 0.0409535143 0.0130708195 0.0085622087 0.0159530702 0.0542946169 0.0054045759 0.0025276980 0.0371020404 0.0793480500 0.0540083424 0.0010592104 0.0036259116 0.0249552645 ;
756 frequency C20pi7 = 0.1634397322 0.0195541184 0.0438701833 0.0374272612 0.0088659891 0.0137554758 0.0220611924 0.5296717726 0.0090006141 0.0017569353 0.0061156267 0.0167117975 0.0029390787 0.0030641349 0.0126457766 0.0829342776 0.0142835614 0.0028640685 0.0032398299 0.0057985736 ;
757 frequency C20pi8 = 0.0917468761 0.0265853306 0.0290699087 0.0133818895 0.0284015012 0.0255084506 0.0196875685 0.0249898794 0.0449766405 0.0583555688 0.1155009222 0.0164915955 0.0395994595 0.0998479096 0.0209916159 0.0736482742 0.0661518462 0.0246463919 0.0972327226 0.0831856483 ;
758 frequency C20pi9 = 0.0646700714 0.0988015996 0.0228907308 0.0168733856 0.0077117603 0.0996414875 0.0544977962 0.0148893975 0.0313851988 0.0505983315 0.1844282999 0.0907931290 0.0774839960 0.0219148172 0.0105004469 0.0321196170 0.0411766062 0.0084303030 0.0206106035 0.0505824221 ;
759 frequency C20pi10 = 0.0135993865 0.0043408375 0.0018469375 0.0007951703 0.0100090240 0.0046420778 0.0018011758 0.0026794645 0.0072401918 0.0814026713 0.3661422246 0.0025158135 0.0734965132 0.2640965246 0.0038994134 0.0043668760 0.0075248451 0.0261564898 0.0660970801 0.0573472826 ;
760 frequency C20pi11 = 0.1478036236 0.0842845089 0.0726630217 0.0534743238 0.0048825808 0.0757166156 0.0727246460 0.0907725939 0.0262288856 0.0035781075 0.0126777221 0.1051660098 0.0059621792 0.0029903868 0.0156558198 0.1459903343 0.0634877444 0.0015928454 0.0050760739 0.0092719768 ;
761 frequency C20pi12 = 0.0186377412 0.0042055165 0.0019865236 0.0008329696 0.0054968852 0.0065890091 0.0020248504 0.0021713483 0.0023665991 0.2020809776 0.4370381920 0.0029120653 0.1241860384 0.0385383157 0.0040672279 0.0046177381 0.0149904396 0.0026871667 0.0056324117 0.1189379840 ;
762 frequency C20pi13 = 0.0477624336 0.0505742667 0.0209574273 0.0141349161 0.0075791708 0.0429296799 0.0462688073 0.0052327914 0.0165351815 0.1741496627 0.1121253570 0.0577575020 0.0330288046 0.0130691347 0.0124374733 0.0264988925 0.0951754678 0.0031660482 0.0112465746 0.2093704079 ;
763 frequency C20pi14 = 0.4164189845 0.0056100821 0.0091701381 0.0045131748 0.0406937949 0.0061320495 0.0063229801 0.0946185184 0.0031057404 0.0076443223 0.0099885414 0.0038941773 0.0069323155 0.0048438356 0.0187840756 0.2360774301 0.0746274607 0.0012172579 0.0034825786 0.0459225422 ;
764 frequency C20pi15 = 0.0402295888 0.0735203003 0.1036647193 0.0365523994 0.0124782975 0.0826558132 0.0372197283 0.0233618081 0.2108307125 0.0093478727 0.0360561493 0.0482410586 0.0100289536 0.0459094917 0.0098503973 0.0533383445 0.0310209005 0.0140076639 0.1064377821 0.0152480184 ;
765 frequency C20pi16 = 0.0323453034 0.0236282995 0.2520448083 0.2431495959 0.0035976296 0.0330831153 0.0710274499 0.1016074562 0.0366225082 0.0031410809 0.0051980542 0.0470129351 0.0024028744 0.0024429276 0.0094837826 0.0848355278 0.0359083275 0.0008730928 0.0067247672 0.0048704638 ;
766 frequency C20pi17 = 0.1476256642 0.0334506604 0.0211972524 0.0403051550 0.0032327194 0.0371554480 0.0576893391 0.0330850942 0.0146392559 0.0108267008 0.0256200793 0.0451350877 0.0058651400 0.0047177179 0.3473710507 0.0892065279 0.0485899446 0.0016358749 0.0044177191 0.0282335685 ;
767 frequency C20pi18 = 0.1031448143 0.0717747663 0.0435172139 0.0386401502 0.0061762467 0.0786603123 0.0923369140 0.0202338419 0.0246761899 0.0376904275 0.0376283678 0.0921698920 0.0161883318 0.0067666433 0.0128302120 0.0951450188 0.1378566702 0.0022144738 0.0083041573 0.0740453560 ;
768 frequency C20pi19 = 0.0837542823 0.0899383244 0.0518811417 0.0804870571 0.0020735078 0.1456497470 0.1947759184 0.0229030361 0.0268458796 0.0074079756 0.0190249576 0.1459287407 0.0067395241 0.0023063393 0.0085616014 0.0455739585 0.0451080843 0.0010771349 0.0049325333 0.0150302559 ;
769 frequency C20pi20 = 0.0578735570 0.0138313604 0.0491421636 0.2946738942 0.0011130839 0.0598250358 0.3402102668 0.0293911435 0.0139817004 0.0030525663 0.0062611922 0.0363365043 0.0027295976 0.0017034884 0.0156106390 0.0358044639 0.0249941878 0.0008664342 0.0038312977 0.0087674229 ;
770
771 [ C20 with fixed weights ]
772 model C20 = POISSON+G+FMIX{C20pi1:1:0.0559910600,C20pi2:1:0.0514824870,C20pi3:1:0.0812922124,C20pi4:1:0.0721976867,C20pi5:1:0.0556718858,C20pi6:1:0.0331003080,C20pi7:1:0.0589501763,C20pi8:1:0.0263756889,C20pi9:1:0.0307584220,C20pi10:1:0.0376701125,C20pi11:1:0.0303058290,C20pi12:1:0.0808775576,C20pi13:1:0.0263349134,C20pi14:1:0.0579101455,C20pi15:1:0.0371248064,C20pi16:1:0.0586867766,C20pi17:1:0.0561479138,C20pi18:1:0.0349810886,C20pi19:1:0.0544937394,C20pi20:1:0.0596471901};
773 [ C20 to weights to be optimized ]
774 model C20Opt = POISSON+G+FMIX{C20pi1,C20pi2,C20pi3,C20pi4,C20pi5,C20pi6,C20pi7,C20pi8,C20pi9,C20pi10,C20pi11,C20pi12,C20pi13,C20pi14,C20pi15,C20pi16,C20pi17,C20pi18,C20pi19,C20pi20};
775
776 model C20Test = POISSON+G+FMIX{C20pi1:1:0.089485,C20pi2:1:0.021281,C20pi3:1:0.119676,C20pi4:1:0.080933,C20pi5:1:0.064054,C20pi6:1:0.021848,C20pi7:1:0.063392,C20pi8:1:0.003629,C20pi9:1:0.007174,C20pi10:1:0.006256,C20pi11:1:0.023424,C20pi12:1:0.086825,C20pi13:1:0.038495,C20pi14:1:0.090028,C20pi15:1:0.020025,C20pi16:1:0.043484,C20pi17:1:0.076864,C20pi18:1:0.031347,C20pi19:1:0.047749,C20pi20:1:0.064031};
777
778 [ ---------------------------------------------------------
779 CAT-C30 profile mixture model of Le, Gascuel & Lartillot (2008)
780 --------------------------------------------------------- ]
781 frequency C30pi1 = 0.1100453954 0.0171294861 0.0640338464 0.1595411459 0.0019047235 0.0310187088 0.1098958823 0.0684301540 0.0137950707 0.0026283074 0.0073396531 0.0358553674 0.0024706414 0.0016629473 0.1669356820 0.1381790473 0.0568342547 0.0004661120 0.0035970152 0.0082365591;
782 frequency C30pi2 = 0.0874125465 0.0806320385 0.0382152368 0.0326119879 0.0049826376 0.0798168854 0.0951700809 0.0144042708 0.0210626652 0.0399884450 0.0301585074 0.1147200015 0.0126488911 0.0048996596 0.0137397028 0.0873769666 0.1558616621 0.0015122843 0.0053974463 0.0793880836;
783 frequency C30pi3 = 0.0225477414 0.0014900535 0.0013034594 0.0005959279 0.0050018158 0.0011436556 0.0015030529 0.0011570953 0.0009374322 0.3944689167 0.0889573138 0.0013600872 0.0189102669 0.0089216031 0.0018312028 0.0028336408 0.0189813395 0.0006693746 0.0023303726 0.4250556480;
784 frequency C30pi4 = 0.0602158209 0.0136833299 0.0414987935 0.2900084105 0.0009525462 0.0621611083 0.3610869026 0.0281925621 0.0130500799 0.0030516237 0.0060401889 0.0352704692 0.0027460635 0.0014625624 0.0127175499 0.0318109377 0.0225279521 0.0007948027 0.0034024563 0.0093258397;
785 frequency C30pi5 = 0.0101223637 0.0028344920 0.0012928910 0.0006379191 0.0085989355 0.0035028551 0.0011249625 0.0024085229 0.0047753376 0.0701153131 0.4135913903 0.0016748492 0.0744862631 0.2785384406 0.0040466582 0.0037087155 0.0052379329 0.0200222636 0.0523938808 0.0408860135;
786 frequency C30pi6 = 0.1335831781 0.0284789590 0.0213891629 0.1125775537 0.0010514541 0.0565844323 0.2099572968 0.0207551870 0.0121330488 0.0073526522 0.0133278240 0.0771772013 0.0030571689 0.0016793592 0.1890195131 0.0484054108 0.0373318180 0.0009266995 0.0026946425 0.0225174379;
787 frequency C30pi7 = 0.0408277374 0.0124491768 0.0080464869 0.0030634898 0.0153918410 0.0102922098 0.0066010880 0.0058113137 0.0245211764 0.1487514547 0.1637802160 0.0075923232 0.0385527359 0.1575049888 0.0058352224 0.0151578617 0.0332220362 0.0264937109 0.1213342989 0.1547706314;
788 frequency C30pi8 = 0.2469059247 0.0106278945 0.0168929681 0.0027418266 0.1039406309 0.0103988197 0.0054944756 0.0373263209 0.0085752319 0.0292403793 0.0535091180 0.0056123053 0.0302246485 0.0251775640 0.0078098946 0.1642352274 0.1239889705 0.0053155877 0.0163953993 0.0955868125;
789 frequency C30pi9 = 0.0549428629 0.1305426495 0.0202957532 0.0092915274 0.0099280995 0.0906036344 0.0417085054 0.0105563869 0.0363512470 0.0569584863 0.1681833183 0.1152521806 0.0592328363 0.0243860149 0.0083055411 0.0283778833 0.0412594019 0.0096355359 0.0249780472 0.0592100878;
790 frequency C30pi10 = 0.0462773303 0.0362984274 0.0412365193 0.0182504174 0.0172727117 0.0348990852 0.0224266258 0.0160971397 0.1357852215 0.0164966886 0.0598936127 0.0239396241 0.0164507129 0.1336320854 0.0117413009 0.0454156401 0.0304387749 0.0330338410 0.2350163763 0.0253978649;
791 frequency C30pi11 = 0.0474379955 0.0410179935 0.0222453982 0.0112116958 0.0082332447 0.0374051414 0.0388100853 0.0055998598 0.0149156570 0.1832173840 0.1100691114 0.0467850545 0.0356443791 0.0116643783 0.0100244663 0.0317171100 0.1114352326 0.0026685586 0.0099660086 0.2199312452;
792 frequency C30pi12 = 0.0213607696 0.0069976154 0.0039878996 0.0012941246 0.0061024858 0.0139566033 0.0036297282 0.0030017014 0.0038425894 0.1309465785 0.4566988203 0.0054567760 0.1947837355 0.0371808169 0.0040747282 0.0076991487 0.0198018718 0.0034086391 0.0064545692 0.0693207986;
793 frequency C30pi13 = 0.0919632044 0.0160004872 0.0764682386 0.0306717360 0.0117031014 0.0160060006 0.0171907654 0.0370684649 0.0100792697 0.0093123713 0.0097240970 0.0205385908 0.0075767282 0.0041589440 0.0179686194 0.3254471625 0.2744377258 0.0013887442 0.0044739725 0.0178217761;
794 frequency C30pi14 = 0.4649246103 0.0043013249 0.0075304815 0.0050731691 0.0233328752 0.0043571322 0.0057994247 0.1495242047 0.0023298425 0.0043361190 0.0055995530 0.0028525398 0.0039313170 0.0025588185 0.0186467246 0.2150194771 0.0477030158 0.0009038096 0.0020087184 0.0292668421;
795 frequency C30pi15 = 0.2051329382 0.0439661329 0.0339418395 0.1070980865 0.0020915940 0.0822742346 0.1989733497 0.0487574293 0.0127143076 0.0058124693 0.0133471767 0.0667787412 0.0043783406 0.0018235059 0.0110997761 0.0873961609 0.0519781961 0.0007361603 0.0023821404 0.0193174204;
796 frequency C30pi16 = 0.0263689890 0.0133613622 0.2727158135 0.3117715371 0.0039462429 0.0218978778 0.0694354212 0.0799842408 0.0309615130 0.0027521242 0.0038579661 0.0288630708 0.0018363656 0.0023351927 0.0062457560 0.0798729385 0.0324143174 0.0007229656 0.0063857732 0.0042705326;
797 frequency C30pi17 = 0.1526502637 0.0332784464 0.0168229991 0.0237392180 0.0040215287 0.0341733672 0.0377949108 0.0306214335 0.0141929803 0.0123317972 0.0290062362 0.0375543022 0.0064473224 0.0058584416 0.3864504800 0.0880336410 0.0489543188 0.0018252558 0.0048877798 0.0313552773;
798 frequency C30pi18 = 0.0080247558 0.0017408595 0.0006327403 0.0003385965 0.0023412143 0.0015507896 0.0007818945 0.0005403825 0.0010026402 0.3177056649 0.3737894172 0.0012598254 0.0488212345 0.0311968471 0.0020687549 0.0012095129 0.0065696791 0.0016309208 0.0043343553 0.1944599147;
799 frequency C30pi19 = 0.0599950319 0.1000540567 0.1334918892 0.0889730776 0.0016884984 0.0864856169 0.0962700957 0.0588796388 0.0327277145 0.0021467269 0.0070876372 0.1825860579 0.0033979446 0.0011800742 0.0141408084 0.0779002375 0.0448817374 0.0006249028 0.0032641120 0.0042241415;
800 frequency C30pi20 = 0.0393520657 0.0838170642 0.1425481600 0.0431197671 0.0099071945 0.1019786610 0.0394639510 0.0282866471 0.2095718357 0.0076101442 0.0258339558 0.0596434088 0.0084586675 0.0188680789 0.0096840517 0.0624998643 0.0347087967 0.0054645779 0.0564145251 0.0127685828;
801 frequency C30pi21 = 0.0072715487 0.0140998918 0.0019756795 0.0027603830 0.0067852535 0.0043339290 0.0025069369 0.0080834718 0.0113217919 0.0056609640 0.0394199644 0.0017735096 0.0079866080 0.1271475634 0.0041098092 0.0052244365 0.0043022271 0.6273570153 0.1084563767 0.0094226397;
802 frequency C30pi22 = 0.0907070068 0.0290062335 0.0860677696 0.0745872716 0.0063699858 0.0259377035 0.0386802115 0.4750046194 0.0168090013 0.0014721054 0.0055149849 0.0343855535 0.0024692074 0.0028859215 0.0112150781 0.0731110371 0.0153705714 0.0022914775 0.0041860660 0.0039281943;
803 frequency C30pi23 = 0.0055291882 0.0024626303 0.0046086594 0.0011413426 0.0072105915 0.0022692184 0.0009683043 0.0016070950 0.0325831191 0.0082918400 0.0353677882 0.0013849437 0.0074486804 0.3744093753 0.0013374573 0.0057402692 0.0037279636 0.0330334445 0.4609978298 0.0098802591;
804 frequency C30pi24 = 0.2443263138 0.0045386562 0.0062422652 0.0031590902 0.0273880205 0.0053593950 0.0076715636 0.0196089609 0.0020189401 0.1017435067 0.0468424225 0.0045492259 0.0201286022 0.0060619450 0.0185219126 0.0497753825 0.1170795523 0.0009577255 0.0035333687 0.3104931504;
805 frequency C30pi25 = 0.0863111274 0.0984811895 0.0313963115 0.0600902926 0.0024419845 0.1672351286 0.2036096150 0.0175221435 0.0245245046 0.0105994220 0.0271209781 0.1485789590 0.0095824358 0.0029393105 0.0068276769 0.0347800318 0.0408210979 0.0014001253 0.0055105388 0.0202271268;
806 frequency C30pi26 = 0.0643926114 0.0369048739 0.1031213278 0.1628208462 0.0023165895 0.0752534859 0.1762701353 0.0297139006 0.0303503732 0.0088163033 0.0148016812 0.0727140107 0.0056748403 0.0043066715 0.0099270322 0.0926433867 0.0833129915 0.0011237109 0.0093801464 0.0161550816;
807 frequency C30pi27 = 0.1736682858 0.0943628709 0.0520404980 0.0285984935 0.0083596568 0.0722446698 0.0483894060 0.0781901497 0.0266134684 0.0068641911 0.0219499324 0.0964011794 0.0112303313 0.0058273974 0.0169661076 0.1547802460 0.0751701930 0.0028774511 0.0082130397 0.0172524320;
808 frequency C30pi28 = 0.0347856579 0.3075984538 0.0314157384 0.0092355245 0.0062754891 0.0861073155 0.0323568406 0.0170288127 0.0306438905 0.0091932292 0.0224428556 0.3020845818 0.0093720833 0.0034303536 0.0104447169 0.0326882932 0.0328713449 0.0025244855 0.0064171317 0.0130832013;
809 frequency C30pi29 = 0.1087737102 0.0051781020 0.0032679768 0.0015823203 0.0247877480 0.0057932006 0.0041769888 0.0134703172 0.0024765788 0.1643462917 0.2337152707 0.0027000391 0.0539213396 0.0316523420 0.0154886946 0.0188187787 0.0474912345 0.0037656478 0.0073106362 0.2512827825;
810 frequency C30pi30 = 0.1101008748 0.0324324597 0.0435098681 0.0579268520 0.0072699765 0.0615196630 0.0828181488 0.0314463068 0.0308557019 0.0530865813 0.1096787834 0.0293860426 0.0458728977 0.0269153699 0.0296430687 0.0715887866 0.0685882454 0.0062324120 0.0257237601 0.0754042006;
811 model C30 = POISSON+G+FMIX{C30pi1:1:0.0095783264,C30pi2:1:0.0248476365,C30pi3:1:0.0636309366,C30pi4:1:0.0537939225,C30pi5:1:0.0295885587,C30pi6:1:0.0117587936,C30pi7:1:0.0132013428,C30pi8:1:0.0236868805,C30pi9:1:0.0261687659,C30pi10:1:0.0239821974,C30pi11:1:0.0257100906,C30pi12:1:0.0465072425,C30pi13:1:0.0546794546,C30pi14:1:0.0536085131,C30pi15:1:0.0270622670,C30pi16:1:0.0403913593,C30pi17:1:0.0474212700,C30pi18:1:0.0458816478,C30pi19:1:0.0214036510,C30pi20:1:0.0290385981,C30pi21:1:0.0123391793,C30pi22:1:0.0569350229,C30pi23:1:0.0419687568,C30pi24:1:0.0339027062,C30pi25:1:0.0388777376,C30pi26:1:0.0196343766,C30pi27:1:0.0233086174,C30pi28:1:0.0622722654,C30pi29:1:0.0184803385,C30pi30:1:0.0203395454};
812
813 [ ---------------------------------------------------------
814 CAT-C40 profile mixture model of Le, Gascuel & Lartillot (2008)
815 --------------------------------------------------------- ]
816 frequency C40pi1 = 0.0660259814 0.0231861755 0.1599815873 0.1054473175 0.0056586745 0.0273928499 0.0440360794 0.0711238664 0.0168194755 0.0039088727 0.0055316013 0.0366689617 0.0037412416 0.0013104807 0.0176359169 0.2497687201 0.1507079582 0.0006723214 0.0038290224 0.0065528958;
817 frequency C40pi2 = 0.0232377444 0.0122683027 0.2759650991 0.3532087982 0.0037987468 0.0197339134 0.0739378219 0.0576668030 0.0315866952 0.0031092806 0.0038711609 0.0259363304 0.0017355634 0.0024032103 0.0063116881 0.0657067704 0.0270483653 0.0007602894 0.0069602476 0.0047531689;
818 frequency C40pi3 = 0.0166486809 0.0012594763 0.0012622242 0.0005651446 0.0036665719 0.0010669784 0.0013356251 0.0008894749 0.0008231853 0.4129367561 0.0884689295 0.0011904105 0.0186054583 0.0082775676 0.0014029981 0.0021339439 0.0162167380 0.0006082049 0.0019553200 0.4206863114;
819 frequency C40pi4 = 0.2394741986 0.0072901253 0.0120536943 0.0044741726 0.0283811727 0.0086558850 0.0105529632 0.0135109628 0.0038929844 0.0765957115 0.0358494908 0.0071093014 0.0199496319 0.0055991131 0.0114265585 0.0847798773 0.1797284519 0.0009838000 0.0042240671 0.2454678377;
820 frequency C40pi5 = 0.1194613086 0.0233255669 0.0294552140 0.0134272792 0.0150526644 0.0301537796 0.0192173037 0.0337675998 0.0214746045 0.0579001821 0.1446308373 0.0147261337 0.0561242940 0.0550467421 0.0631355418 0.0925266727 0.0831230185 0.0131636136 0.0331118002 0.0811758434;
821 frequency C40pi6 = 0.0567043710 0.0117359330 0.0364734454 0.2955500969 0.0008924801 0.0609516515 0.3795154126 0.0230469606 0.0118360971 0.0031182036 0.0060137466 0.0314205689 0.0028584065 0.0012972333 0.0124745819 0.0300334889 0.0227051137 0.0007738758 0.0031343761 0.0094639563;
822 frequency C40pi7 = 0.0179027412 0.0040967133 0.0035697688 0.0008870412 0.0160760340 0.0045395474 0.0023182113 0.0039829808 0.0127292680 0.0404650518 0.1676143477 0.0027994718 0.0424172255 0.3344862590 0.0020115128 0.0075841581 0.0068227293 0.0518381385 0.2452542553 0.0326045442;
823 frequency C40pi8 = 0.2712170094 0.0056480837 0.0141045260 0.0021017036 0.2003830179 0.0048264059 0.0023229984 0.0502501222 0.0053727960 0.0150684657 0.0330003443 0.0020646283 0.0154811217 0.0202990358 0.0045351023 0.1764198412 0.0839578061 0.0046265242 0.0141271048 0.0741933626;
824 frequency C40pi9 = 0.0894736584 0.1040026384 0.0190192153 0.0272183085 0.0045538316 0.1168091917 0.1275076663 0.0115685734 0.0215746293 0.0469424171 0.0512035100 0.1382047308 0.0147656854 0.0056590176 0.0095546504 0.0383953611 0.0836652641 0.0017079427 0.0062181292 0.0819555787;
825 frequency C40pi10 = 0.0495441385 0.0375345822 0.0315863530 0.0143641284 0.0182505609 0.0316504100 0.0215379122 0.0140199913 0.1108543799 0.0247065801 0.0700287927 0.0258142032 0.0188271760 0.1418048822 0.0112101202 0.0456094427 0.0361427973 0.0371985427 0.2223972375 0.0369177689;
826 frequency C40pi11 = 0.1704314254 0.0415784004 0.0271109259 0.1098556600 0.0009747331 0.0917299929 0.2536458944 0.0249846466 0.0101389736 0.0058749399 0.0116526350 0.0903324267 0.0036512738 0.0013321301 0.0293613681 0.0561765645 0.0479045729 0.0006696817 0.0022637316 0.0203300232;
827 frequency C40pi12 = 0.0162725399 0.0054826071 0.0021876158 0.0010182101 0.0050614097 0.0104414465 0.0025141347 0.0021935389 0.0029914328 0.1328173512 0.4904441779 0.0040120394 0.1929931280 0.0376245580 0.0034333187 0.0040122105 0.0127074428 0.0032107554 0.0058100621 0.0647720205;
828 frequency C40pi13 = 0.0823765743 0.0734226431 0.0598389731 0.0311745159 0.0065694304 0.0686451074 0.0675530778 0.0178961594 0.0251143622 0.0291161743 0.0287904106 0.0982301674 0.0168022878 0.0064717899 0.0114044922 0.1302995288 0.1820374273 0.0022724618 0.0079573279 0.0540270885;
829 frequency C40pi14 = 0.3594965940 0.0072407229 0.0033421456 0.0031484357 0.0251417178 0.0049014279 0.0064962700 0.1194682267 0.0022970448 0.0458766662 0.0468053893 0.0050168849 0.0215568816 0.0092020461 0.0443915884 0.0465270945 0.0477755293 0.0024540215 0.0046450361 0.1942162766;
830 frequency C40pi15 = 0.2015583874 0.0430161610 0.0425386444 0.0954149893 0.0032365302 0.0772010857 0.1534908791 0.0667291678 0.0155218808 0.0067740832 0.0165114429 0.0547322644 0.0060162992 0.0025643300 0.0091970560 0.1185981804 0.0625472744 0.0009565508 0.0031150007 0.0202797924;
831 frequency C40pi16 = 0.1042731047 0.0147062345 0.0621645800 0.2424069523 0.0022450116 0.0356498946 0.1774821588 0.1697819523 0.0132648834 0.0018929517 0.0042542620 0.0220651981 0.0016441234 0.0012570256 0.0317041583 0.0778636230 0.0288515782 0.0006930898 0.0017741945 0.0060250231;
832 frequency C40pi17 = 0.0781183281 0.0111498472 0.0159270309 0.0041541669 0.0194448667 0.0240151620 0.0116633921 0.0111524105 0.0063589385 0.1354530457 0.2457574952 0.0093729846 0.1087781166 0.0262793949 0.0055294038 0.0408518858 0.0860514305 0.0031547586 0.0085108496 0.1482764918;
833 frequency C40pi18 = 0.0856592432 0.0101233167 0.0441923073 0.0135061568 0.0136072878 0.0092590642 0.0078602552 0.0245400880 0.0055379075 0.0100591561 0.0103343559 0.0127318506 0.0080675803 0.0047153035 0.0175273997 0.3406479487 0.3573294650 0.0014243098 0.0035099810 0.0193670227;
834 frequency C40pi19 = 0.0674594695 0.1161734658 0.1163107783 0.0662588409 0.0021634231 0.0939360452 0.0865501280 0.0368556575 0.0381149118 0.0033238825 0.0093839985 0.1899736999 0.0039487389 0.0018212730 0.0151207830 0.0842204423 0.0565953680 0.0007187305 0.0046189437 0.0064514195;
835 frequency C40pi20 = 0.0572262322 0.0494723554 0.1083882793 0.1793932771 0.0015301521 0.0903668522 0.1992261265 0.0316472274 0.0291392067 0.0045804559 0.0100739563 0.1015624916 0.0040204606 0.0013701849 0.0063674130 0.0621142922 0.0496102162 0.0006669285 0.0046497641 0.0085941279;
836 frequency C40pi21 = 0.0036020163 0.0102712927 0.0013455508 0.0020871647 0.0045484804 0.0032718114 0.0017857730 0.0056391633 0.0064968790 0.0029292916 0.0232635081 0.0010419846 0.0044592278 0.0855714596 0.0024991984 0.0030671803 0.0025900250 0.7617821954 0.0678809532 0.0058668443;
837 frequency C40pi22 = 0.2032018418 0.0083895722 0.0143743754 0.0135011707 0.0098131618 0.0044514580 0.0083818173 0.6184886075 0.0027747899 0.0011828492 0.0039826789 0.0044598895 0.0020631785 0.0019619615 0.0085870399 0.0739919851 0.0108922273 0.0018606145 0.0015638674 0.0060769136;
838 frequency C40pi23 = 0.0050898779 0.0028740788 0.0057092962 0.0016126151 0.0061776450 0.0024693148 0.0012040415 0.0016334183 0.0393460780 0.0059088776 0.0249343597 0.0013713662 0.0049795162 0.3563126947 0.0014136424 0.0059527667 0.0036536770 0.0357987380 0.4853645852 0.0081934106;
839 frequency C40pi24 = 0.0403335679 0.0540186397 0.0216052457 0.0098218598 0.0081549541 0.0383639077 0.0375406578 0.0047934404 0.0176735565 0.1893424159 0.1051859862 0.0607377395 0.0305599836 0.0119140782 0.0077550551 0.0257110173 0.1009913165 0.0028780020 0.0115276935 0.2210908828;
840 frequency C40pi25 = 0.0790086293 0.1065441152 0.0309384274 0.0546012394 0.0024947877 0.1843375981 0.1997882784 0.0192655847 0.0270700474 0.0075667489 0.0254542392 0.1553108816 0.0098024439 0.0023773444 0.0056640684 0.0332370813 0.0359574739 0.0011682801 0.0048820809 0.0145306498;
841 frequency C40pi26 = 0.0722240672 0.0489728405 0.0678929607 0.1194883992 0.0064755348 0.0708969573 0.1345886574 0.0287815397 0.0699011334 0.0173588702 0.0519870084 0.0490341790 0.0154411043 0.0348233029 0.0145597486 0.0589579876 0.0425972780 0.0087913770 0.0554386705 0.0317883834;
842 frequency C40pi27 = 0.1085842431 0.0206450023 0.0441956285 0.1529666596 0.0012502570 0.0405398136 0.1664851192 0.0336098469 0.0134902179 0.0038821795 0.0089861440 0.0576227094 0.0024339036 0.0014553522 0.1990095021 0.0846749753 0.0454715217 0.0005902831 0.0027650162 0.0113416246;
843 frequency C40pi28 = 0.0309526387 0.3195887318 0.0301336637 0.0082352132 0.0065593963 0.0832608108 0.0291974083 0.0154206187 0.0310385092 0.0098251607 0.0237900204 0.3062634996 0.0097071728 0.0036891639 0.0095029109 0.0295285439 0.0303052301 0.0028125285 0.0068850639 0.0133037148;
844 frequency C40pi29 = 0.0098953741 0.0019604525 0.0007307935 0.0003748228 0.0028276741 0.0017337004 0.0009182100 0.0006997068 0.0010419482 0.3115040359 0.3750387796 0.0013960508 0.0474451070 0.0298607430 0.0025296256 0.0014628019 0.0075738968 0.0016799771 0.0040259930 0.1973003069;
845 frequency C40pi30 = 0.1163213921 0.0273321006 0.0250163656 0.0731917718 0.0034792282 0.0586677248 0.1380880502 0.0193193469 0.0160240740 0.0712243431 0.0771473538 0.0355120487 0.0242841072 0.0094117688 0.0508926833 0.0475560280 0.0726552233 0.0026892716 0.0076166020 0.1235705162;
846 frequency C40pi31 = 0.1285218235 0.0373073487 0.1179844215 0.0402749992 0.0172928883 0.0439706110 0.0250692272 0.1127033137 0.0606981059 0.0109350265 0.0258415767 0.0288749652 0.0167592956 0.0199118302 0.0180674983 0.1741489481 0.0648967655 0.0063574951 0.0321771650 0.0182066946;
847 frequency C40pi32 = 0.0372286941 0.0094528028 0.0053377315 0.0023703173 0.0144940088 0.0079097138 0.0048585146 0.0046433943 0.0186795102 0.1820459527 0.1780099317 0.0058198481 0.0371334296 0.1463772419 0.0048538601 0.0103570678 0.0284161577 0.0211293603 0.0958905187 0.1849919442;
848 frequency C40pi33 = 0.0535643726 0.1159797757 0.0239172676 0.0113537364 0.0096256227 0.0928585070 0.0391699080 0.0120279334 0.0384887950 0.0522748270 0.1892392595 0.0996037748 0.0712219098 0.0264213736 0.0083720574 0.0299114019 0.0389484845 0.0104232046 0.0265030050 0.0500947835;
849 frequency C40pi34 = 0.1332424803 0.0033147683 0.0022704992 0.0012739239 0.0246514263 0.0030843469 0.0040461524 0.0089139209 0.0015864680 0.1971284995 0.1251288442 0.0023713225 0.0286947200 0.0156995251 0.0118845743 0.0171461828 0.0563298009 0.0017341820 0.0048778410 0.3566205216;
850 frequency C40pi35 = 0.1498658185 0.0326607222 0.0176452820 0.0280354786 0.0035437399 0.0348151308 0.0435380704 0.0311112643 0.0140625707 0.0101953314 0.0251433928 0.0393124980 0.0051548319 0.0047533945 0.3923800449 0.0874496981 0.0473306717 0.0015215239 0.0043208299 0.0271597054;
851 frequency C40pi36 = 0.4214366359 0.0061425967 0.0121590498 0.0073305074 0.0187609694 0.0072748556 0.0086837775 0.0902333103 0.0030262044 0.0039362777 0.0047193320 0.0051508681 0.0038306586 0.0027156136 0.0208940236 0.2901188793 0.0651922314 0.0008108235 0.0023622848 0.0252211004;
852 frequency C40pi37 = 0.1770713890 0.1332782050 0.0311656783 0.0226500225 0.0078348946 0.0752471493 0.0509767242 0.0897389513 0.0220667143 0.0059519850 0.0205369728 0.1257689326 0.0092982479 0.0040514178 0.0264087912 0.1169591448 0.0565566955 0.0029947127 0.0049346701 0.0165087010;
853 frequency C40pi38 = 0.0293984032 0.0370901720 0.1483622633 0.1099709900 0.0031729093 0.0388688450 0.0464270335 0.4222420155 0.0272494642 0.0007997326 0.0037634298 0.0622314461 0.0016657052 0.0015039626 0.0056481827 0.0472252404 0.0086568982 0.0009176022 0.0027693124 0.0020363920;
854 frequency C40pi39 = 0.0265779317 0.0791104753 0.1318603134 0.0280314140 0.0101369144 0.0989710810 0.0269057233 0.0173376629 0.2815133703 0.0064646977 0.0268210053 0.0474749135 0.0072375268 0.0276960902 0.0083014995 0.0426276702 0.0259042511 0.0078528946 0.0891598394 0.0100147256;
855 frequency C40pi40 = 0.0096096503 0.0027136180 0.0013104432 0.0006331856 0.0077301682 0.0033899420 0.0010471898 0.0020227436 0.0039001415 0.0733098005 0.4451691588 0.0014931484 0.0732575295 0.2630171690 0.0042768091 0.0036117358 0.0057928403 0.0181275729 0.0370698053 0.0425173480;
856 model C40 = POISSON+G+FMIX{C40pi1:1:0.0223853788,C40pi2:1:0.0338891820,C40pi3:1:0.0577169375,C40pi4:1:0.0252416233,C40pi5:1:0.0108607921,C40pi6:1:0.0462373793,C40pi7:1:0.0102293175,C40pi8:1:0.0147523625,C40pi9:1:0.0143161352,C40pi10:1:0.0182302541,C40pi11:1:0.0204025079,C40pi12:1:0.0425505156,C40pi13:1:0.0248627269,C40pi14:1:0.0105892988,C40pi15:1:0.0188238725,C40pi16:1:0.0086663445,C40pi17:1:0.0148496147,C40pi18:1:0.0343037402,C40pi19:1:0.0225335203,C40pi20:1:0.0174068578,C40pi21:1:0.0112207827,C40pi22:1:0.0443532245,C40pi23:1:0.0392573370,C40pi24:1:0.0196756555,C40pi25:1:0.0287690328,C40pi26:1:0.0114441177,C40pi27:1:0.0112338740,C40pi28:1:0.0582694099,C40pi29:1:0.0444272279,C40pi30:1:0.0112010942,C40pi31:1:0.0145176111,C40pi32:1:0.0114629026,C40pi33:1:0.0239628061,C40pi34:1:0.0266266492,C40pi35:1:0.0481201159,C40pi36:1:0.0371147423,C40pi37:1:0.0160476688,C40pi38:1:0.0237249267,C40pi39:1:0.0235226203,C40pi40:1:0.0261998398};
857
858 [ ---------------------------------------------------------
859 CAT-C50 profile mixture model of Le, Gascuel & Lartillot (2008)
860 --------------------------------------------------------- ]
861 frequency C50pi1 = 0.1357566757 0.0328511938 0.0937692919 0.0757182069 0.0041887049 0.0448010470 0.0572805366 0.1210866186 0.0167465028 0.0049719235 0.0113823284 0.0458096069 0.0064563157 0.0029292810 0.0228705187 0.2060115780 0.1011347978 0.0012443033 0.0056104605 0.0093801079;
862 frequency C50pi2 = 0.0530862751 0.1905936010 0.0595772279 0.0320970468 0.0026608079 0.1152605895 0.0840617877 0.0196495178 0.0274729775 0.0064919200 0.0158709120 0.2635539775 0.0078171228 0.0017231166 0.0121639300 0.0449347664 0.0472425608 0.0008407188 0.0037608716 0.0111402722;
863 frequency C50pi3 = 0.0083279799 0.0007172026 0.0006359642 0.0003134388 0.0020547407 0.0007351595 0.0005373710 0.0005576905 0.0004858721 0.4370910601 0.1208722220 0.0006394909 0.0195499664 0.0090175268 0.0007265254 0.0007876194 0.0057076665 0.0006453449 0.0016797264 0.3889174318;
864 frequency C50pi4 = 0.2072868350 0.0166858699 0.0129177658 0.0020625574 0.0849982226 0.0151757635 0.0065903656 0.0472047575 0.0130289256 0.0345690755 0.1042722764 0.0075861385 0.0498042308 0.0572909747 0.0064928361 0.1183618036 0.0780339514 0.0128352368 0.0323576924 0.0924447209;
865 frequency C50pi5 = 0.0364181183 0.0076427099 0.0052725527 0.0020389950 0.0171009943 0.0064088232 0.0042399368 0.0053824238 0.0198596156 0.1361523026 0.1651892915 0.0045481616 0.0387479055 0.2025922657 0.0055053348 0.0121111950 0.0254621828 0.0327580458 0.1368025306 0.1357666147;
866 frequency C50pi6 = 0.0535489196 0.0099543365 0.0269073208 0.3076150732 0.0007101021 0.0574988641 0.4066173371 0.0204537673 0.0096286483 0.0025879708 0.0049721459 0.0280989086 0.0025143457 0.0010618006 0.0124317994 0.0247246015 0.0191107367 0.0006385967 0.0024132214 0.0085115039;
867 frequency C50pi7 = 0.0074733729 0.0025226602 0.0033967505 0.0005574007 0.0081158286 0.0037658904 0.0013610444 0.0022017759 0.0115142679 0.0195730439 0.1268878488 0.0018497296 0.0269141680 0.3821985941 0.0019970421 0.0057127939 0.0039692337 0.0553575998 0.3184099394 0.0162210153;
868 frequency C50pi8 = 0.2615592974 0.0027098854 0.0124908261 0.0020153852 0.2740228527 0.0017043893 0.0007667803 0.0463498030 0.0019474361 0.0082858275 0.0147048711 0.0010787235 0.0063051368 0.0062080862 0.0039442437 0.1940042648 0.0963699489 0.0016185483 0.0048431386 0.0590705550;
869 frequency C50pi9 = 0.1190557043 0.0956320251 0.0215995297 0.0378323341 0.0041536088 0.1151348174 0.1337084452 0.0179375220 0.0216767047 0.0336228770 0.0557402194 0.1132452331 0.0178407325 0.0063405927 0.0147606946 0.0478666925 0.0712091035 0.0022867238 0.0075728630 0.0627835766;
870 frequency C50pi10 = 0.0505010344 0.0281381134 0.0341872191 0.0178157543 0.0183140005 0.0271729546 0.0212018661 0.0176052654 0.1190104107 0.0161645217 0.0561232531 0.0203908848 0.0146521042 0.1553484132 0.0135251600 0.0478959652 0.0292963208 0.0376058633 0.2477283800 0.0273225153;
871 frequency C50pi11 = 0.1239446910 0.0355525870 0.0409769096 0.1479953346 0.0011563976 0.0908869312 0.2700270273 0.0283589709 0.0126760201 0.0064825033 0.0122101302 0.0787433823 0.0042467440 0.0016540857 0.0205717500 0.0552940245 0.0474239965 0.0008596621 0.0027823209 0.0181565313;
872 frequency C50pi12 = 0.0160542063 0.0027359185 0.0014708079 0.0007004900 0.0034820152 0.0061470051 0.0016359686 0.0022137927 0.0013207229 0.1640035117 0.4616043506 0.0021342205 0.2174099502 0.0143751693 0.0013694259 0.0037614383 0.0172651408 0.0011454338 0.0019438536 0.0792265779;
873 frequency C50pi13 = 0.1548192401 0.0131324559 0.0280584102 0.0095301620 0.0166267416 0.0175228950 0.0170969133 0.0179616718 0.0078385586 0.0865181208 0.0523369910 0.0132802182 0.0326348210 0.0083511229 0.0145594414 0.1096327081 0.2218108602 0.0015829972 0.0062173360 0.1704883347;
874 frequency C50pi14 = 0.2950313592 0.0027580697 0.0021616268 0.0015364190 0.0375439186 0.0028808733 0.0042976283 0.0261726702 0.0008294969 0.0834938143 0.0553606311 0.0022642314 0.0181259911 0.0074433078 0.0126794048 0.0382913338 0.0783205173 0.0010015148 0.0034016419 0.3264055498;
875 frequency C50pi15 = 0.1683177099 0.0820396152 0.0526048706 0.0822517150 0.0023029997 0.0969341246 0.1488943001 0.0535291188 0.0179803231 0.0032503636 0.0114941086 0.1156402642 0.0039439899 0.0015002945 0.0066854154 0.0924511658 0.0480769504 0.0006152103 0.0025022919 0.0089851683;
876 frequency C50pi16 = 0.0334088176 0.0134485791 0.1590918150 0.3657542471 0.0025127086 0.0327665151 0.1820739351 0.0740807194 0.0202010901 0.0016650025 0.0036700956 0.0295517886 0.0017087810 0.0011422805 0.0073155123 0.0426788071 0.0211162106 0.0005931485 0.0034724580 0.0037474882;
877 frequency C50pi17 = 0.0777586977 0.0174438357 0.0053423343 0.0043431532 0.0062523949 0.0220851281 0.0161769285 0.0053903202 0.0080675581 0.1052945216 0.1617365895 0.0148319919 0.0288253912 0.0168985297 0.2565426868 0.0202089662 0.0542929694 0.0060146095 0.0078109966 0.1646823969;
878 frequency C50pi18 = 0.0727013979 0.0048977192 0.0026095383 0.0011420120 0.0198747408 0.0066949336 0.0030401434 0.0079074845 0.0026492900 0.1685788878 0.3185489163 0.0026024909 0.0735597038 0.0490419983 0.0051699104 0.0128630830 0.0305356924 0.0050857840 0.0095279173 0.2029683559;
879 frequency C50pi19 = 0.0658153836 0.0833432992 0.0224582275 0.0107735824 0.0092974677 0.0745951987 0.0299754097 0.0146336557 0.0148026634 0.0671888719 0.2198675990 0.0868172087 0.1084156835 0.0155812696 0.0071132147 0.0381451947 0.0562948237 0.0056421684 0.0102813038 0.0589577740;
880 frequency C50pi20 = 0.0525278351 0.0364897390 0.0903013988 0.1854660991 0.0037795400 0.0776857292 0.1789287290 0.0232011648 0.0687702011 0.0135825419 0.0337350646 0.0458143770 0.0108457797 0.0191020037 0.0088729983 0.0495289201 0.0389358438 0.0046292762 0.0354195947 0.0223831639;
881 frequency C50pi21 = 0.0026515970 0.0080885204 0.0010572021 0.0016052142 0.0036540307 0.0022979498 0.0014681767 0.0046230912 0.0043887616 0.0020669456 0.0172444871 0.0006593575 0.0034691503 0.0658351447 0.0019185467 0.0022498420 0.0021278866 0.8183345006 0.0515918357 0.0046677595;
882 frequency C50pi22 = 0.0548133174 0.0692044159 0.0211265710 0.0207779125 0.0072646572 0.0567865657 0.0738456579 0.0051797705 0.0168408457 0.1386104888 0.0713795154 0.0896393340 0.0201205491 0.0082150393 0.0104049016 0.0282344422 0.0995597110 0.0019722093 0.0074054035 0.1986186919;
883 frequency C50pi23 = 0.0047955268 0.0028033787 0.0050506238 0.0014080516 0.0061671241 0.0019350126 0.0009861551 0.0014396818 0.0389623239 0.0048950388 0.0151748150 0.0012306644 0.0032520404 0.3601993060 0.0011266316 0.0054509935 0.0034763921 0.0362899931 0.4980200998 0.0073361467;
884 frequency C50pi24 = 0.0365462996 0.0280070630 0.0183606115 0.0070525803 0.0093251684 0.0300239431 0.0221812842 0.0047778642 0.0178840316 0.2025947306 0.1973012130 0.0250209750 0.0557862640 0.0258067541 0.0042772210 0.0209374223 0.0731398943 0.0049738166 0.0200601168 0.1959427463;
885 frequency C50pi25 = 0.0684197684 0.0111619750 0.0544764241 0.0224313301 0.0106958312 0.0091799953 0.0097436799 0.0255871619 0.0055558006 0.0059416697 0.0076746853 0.0144198991 0.0056892166 0.0037356845 0.0172554137 0.3527301149 0.3586913194 0.0012501907 0.0028636710 0.0124961682;
886 frequency C50pi26 = 0.0495330775 0.1060064564 0.1511923969 0.0483471288 0.0080946362 0.0886108407 0.0449556763 0.0331436148 0.1447288287 0.0061850770 0.0190407203 0.0948075276 0.0063418871 0.0126162987 0.0100869563 0.0799801169 0.0445418973 0.0044765096 0.0363930724 0.0109172804;
887 frequency C50pi27 = 0.0702411901 0.0642050323 0.0779553908 0.0510328304 0.0042438849 0.0723300485 0.0883747710 0.0177347101 0.0233800891 0.0198779320 0.0183537117 0.1051267065 0.0107865869 0.0037987118 0.0112811107 0.1345081583 0.1805543234 0.0014252764 0.0055089381 0.0392805971;
888 frequency C50pi28 = 0.1207399152 0.1741788075 0.0385528120 0.0162689581 0.0118494185 0.0760068404 0.0337935391 0.0653431008 0.0342783806 0.0085426053 0.0256788075 0.1434443984 0.0112347894 0.0061270793 0.0294493558 0.1091415488 0.0634181251 0.0046156419 0.0085374279 0.0187984481;
889 frequency C50pi29 = 0.0064521696 0.0021817337 0.0005939658 0.0003904032 0.0021538307 0.0019099968 0.0008007758 0.0005208471 0.0011374294 0.2850758996 0.4278536740 0.0013920239 0.0561988528 0.0449501501 0.0026289702 0.0011053664 0.0055157148 0.0022753671 0.0059612583 0.1509015707;
890 frequency C50pi30 = 0.0969092741 0.0359723370 0.0633194168 0.0411020773 0.0145578946 0.0466661704 0.0469223767 0.0374614202 0.0537149580 0.0394603009 0.0856256544 0.0283577862 0.0346435320 0.0507298072 0.0167177549 0.0990945318 0.0806503833 0.0128373826 0.0598972198 0.0553597218;
891 frequency C50pi31 = 0.0840212010 0.0214242172 0.2240668646 0.0354684798 0.0265031681 0.0235675678 0.0076026464 0.1173325117 0.0516019781 0.0048917455 0.0067211727 0.0173653354 0.0079342101 0.0087501486 0.0093276105 0.2637097946 0.0630157977 0.0022314593 0.0170994247 0.0073646661;
892 frequency C50pi32 = 0.0055061507 0.0012508737 0.0004824961 0.0004530173 0.0054435931 0.0011315076 0.0004150379 0.0012285001 0.0019884532 0.0617431901 0.4342418135 0.0008161868 0.0554628445 0.3289659386 0.0025814794 0.0021197505 0.0029510440 0.0172981374 0.0412097497 0.0347102358;
893 frequency C50pi33 = 0.0442014612 0.1295816316 0.0258622052 0.0148900471 0.0076165815 0.1301765579 0.0636708052 0.0105339122 0.0662542863 0.0423977240 0.1434197528 0.1040381429 0.0403363621 0.0260540342 0.0089335090 0.0242573966 0.0317938092 0.0077831996 0.0309973779 0.0472012033;
894 frequency C50pi34 = 0.0571984155 0.0034929878 0.0031324721 0.0012472712 0.0113230439 0.0025279922 0.0040737817 0.0030647398 0.0020494153 0.3131200932 0.0901750144 0.0034699557 0.0242565205 0.0112345295 0.0048197020 0.0095675953 0.0529842025 0.0010645104 0.0041851135 0.3970126433;
895 frequency C50pi35 = 0.1141963934 0.0102229903 0.0178644126 0.0172307307 0.0056978908 0.0039055039 0.0085974326 0.7425714921 0.0026414175 0.0005602022 0.0019872568 0.0055400059 0.0004739977 0.0010663175 0.0054302447 0.0508318204 0.0055408544 0.0018890811 0.0012409205 0.0025110348;
896 frequency C50pi36 = 0.3531758625 0.0043402857 0.0031812423 0.0030024877 0.0165711581 0.0029126214 0.0042077690 0.4520896100 0.0021366362 0.0063692579 0.0120143269 0.0022586970 0.0080260130 0.0043865828 0.0111462027 0.0658344033 0.0182952730 0.0010872878 0.0023330172 0.0266312657;
897 frequency C50pi37 = 0.0310798708 0.0234519814 0.1273669012 0.1197925100 0.0031216960 0.0295858842 0.0470763446 0.4883046368 0.0193412101 0.0008855622 0.0032808220 0.0408430573 0.0014984226 0.0016298596 0.0063229464 0.0423452622 0.0082797260 0.0007718998 0.0024996877 0.0025217188;
898 frequency C50pi38 = 0.0370340667 0.0689410214 0.1704407181 0.1041817082 0.0018108784 0.0715495095 0.0659866718 0.2159298358 0.0443591808 0.0008668888 0.0064679416 0.1275300877 0.0027248464 0.0014178323 0.0060253154 0.0534574556 0.0147073432 0.0007999410 0.0037708147 0.0019979426;
899 frequency C50pi39 = 0.0160398536 0.0526622999 0.1051167149 0.0187352256 0.0085330116 0.0922616498 0.0154450839 0.0076235155 0.3848449137 0.0057129406 0.0277195224 0.0219347380 0.0071078308 0.0376358992 0.0072201969 0.0209969653 0.0142198783 0.0096946226 0.1384243143 0.0080708232;
900 frequency C50pi40 = 0.0165549167 0.0085856833 0.0049441851 0.0016567380 0.0086529073 0.0184087838 0.0033759867 0.0033844413 0.0084695063 0.0483923758 0.4963073963 0.0056997331 0.1949377866 0.0999527140 0.0060271256 0.0084289585 0.0122619536 0.0114013282 0.0192314834 0.0233259964;
901 frequency C50pi41 = 0.0227379959 0.0137060298 0.3162561805 0.2932103363 0.0037073869 0.0169119273 0.0380984220 0.0550224760 0.0319886436 0.0039219190 0.0041582288 0.0312539900 0.0019467591 0.0022276545 0.0059660826 0.0998736999 0.0462336456 0.0007310446 0.0069012376 0.0051463400;
902 frequency C50pi42 = 0.2406936002 0.0197081082 0.0462578641 0.0206379264 0.0186726798 0.0189843646 0.0129785315 0.1749109142 0.0118714342 0.0049349532 0.0126237761 0.0127876711 0.0095642661 0.0083606873 0.0326283314 0.2101300187 0.1130042042 0.0041951500 0.0069210515 0.0201344675;
903 frequency C50pi43 = 0.0214325714 0.3730744306 0.0220674626 0.0037495290 0.0069038342 0.0670391950 0.0159298773 0.0126211348 0.0284477629 0.0102051798 0.0242954287 0.3272456489 0.0093147452 0.0036403029 0.0070138928 0.0216860624 0.0232259733 0.0030422478 0.0065368590 0.0125278613;
904 frequency C50pi44 = 0.1567707052 0.0258059606 0.0161658338 0.0223946414 0.0074382689 0.0274455582 0.0410010574 0.0360501033 0.0159972680 0.0640941463 0.0944756654 0.0192586366 0.0312789234 0.0227728534 0.1653169011 0.0640177954 0.0549103568 0.0050980224 0.0138248643 0.1158824381;
905 frequency C50pi45 = 0.4345912387 0.0061142999 0.0097660767 0.0060102195 0.0197377879 0.0069062805 0.0082800652 0.0829075516 0.0029125126 0.0047747098 0.0054182241 0.0049974525 0.0039676868 0.0029052002 0.0193588692 0.2795854727 0.0677816788 0.0008196092 0.0025196339 0.0306454302;
906 frequency C50pi46 = 0.0296734965 0.1443250343 0.0128668160 0.0059561454 0.0129805897 0.0492311054 0.0262726056 0.0069437743 0.0676183913 0.0452364160 0.1374511139 0.0907089722 0.0308070846 0.0816441785 0.0060701025 0.0197130339 0.0299715868 0.0461468661 0.1119414237 0.0444412635;
907 frequency C50pi47 = 0.1089911217 0.0159187676 0.0643054232 0.2086425054 0.0016540963 0.0375565797 0.1791004993 0.0610564917 0.0144660242 0.0038322948 0.0067778708 0.0372270242 0.0022817918 0.0012634818 0.0851792013 0.1065821239 0.0524401536 0.0005901255 0.0027836060 0.0093508169;
908 frequency C50pi48 = 0.1429463629 0.0304191716 0.0191145368 0.0351867799 0.0031493079 0.0341248336 0.0508492526 0.0305914291 0.0134276644 0.0070227247 0.0197257013 0.0421442438 0.0038904796 0.0040697467 0.4052202085 0.0874406009 0.0445304918 0.0012842531 0.0039485525 0.0209136585;
909 frequency C50pi49 = 0.0580116857 0.0903213669 0.0369245281 0.0613603988 0.0022829951 0.2073851382 0.2225853236 0.0159476910 0.0311816018 0.0068543753 0.0217092509 0.1504781849 0.0084841006 0.0020581132 0.0046206107 0.0276754451 0.0321477211 0.0011651089 0.0051889637 0.0136173964;
910 frequency C50pi50 = 0.2153540940 0.0359173007 0.0219927944 0.0735128474 0.0037017294 0.0566408566 0.1350375818 0.0662986417 0.0157121780 0.0138456188 0.0266922211 0.0474338339 0.0088042600 0.0035035311 0.0739583083 0.0921989198 0.0575687235 0.0019306896 0.0044520833 0.0454437865;
911 model C50 = POISSON+G+FMIX{C50pi1:1:0.0164297003,C50pi2:1:0.0273175755,C50pi3:1:0.0460247610,C50pi4:1:0.0084864734,C50pi5:1:0.0125389252,C50pi6:1:0.0343549036,C50pi7:1:0.0130241102,C50pi8:1:0.0094755681,C50pi9:1:0.0190040551,C50pi10:1:0.0151902354,C50pi11:1:0.0320534760,C50pi12:1:0.0210059850,C50pi13:1:0.0237408547,C50pi14:1:0.0239841203,C50pi15:1:0.0213748021,C50pi16:1:0.0210717705,C50pi17:1:0.0050241805,C50pi18:1:0.0166262276,C50pi19:1:0.0143945956,C50pi20:1:0.0104391130,C50pi21:1:0.0107628277,C50pi22:1:0.0148818171,C50pi23:1:0.0321480239,C50pi24:1:0.0145477978,C50pi25:1:0.0332355807,C50pi26:1:0.0143190281,C50pi27:1:0.0234478734,C50pi28:1:0.0183044983,C50pi29:1:0.0403269452,C50pi30:1:0.0135629530,C50pi31:1:0.0091880799,C50pi32:1:0.0158270022,C50pi33:1:0.0121019379,C50pi34:1:0.0353560982,C50pi35:1:0.0404495617,C50pi36:1:0.0104569232,C50pi37:1:0.0146187792,C50pi38:1:0.0093984095,C50pi39:1:0.0146773809,C50pi40:1:0.0201635562,C50pi41:1:0.0255640273,C50pi42:1:0.0039486842,C50pi43:1:0.0393652608,C50pi44:1:0.0056415419,C50pi45:1:0.0382833580,C50pi46:1:0.0039735086,C50pi47:1:0.0140269355,C50pi48:1:0.0476703673,C50pi49:1:0.0204062788,C50pi50:1:0.0117835304};
912
913 [ ---------------------------------------------------------
914 CAT-C60 profile mixture model of Le, Gascuel & Lartillot (2008)
915 --------------------------------------------------------- ]
916 frequency C60pi1 = 0.1534363248 0.0444389067 0.0796726990 0.0546757288 0.0047306596 0.0514333025 0.0529324359 0.1103775749 0.0174480218 0.0050343887 0.0130294160 0.0603928711 0.0075550589 0.0035554315 0.0249523704 0.2029625968 0.0957668473 0.0014444483 0.0059800307 0.0101808864;
917 frequency C60pi2 = 0.0281984692 0.3031055487 0.0312954609 0.0091549350 0.0019503463 0.0939884393 0.0388530140 0.0084028325 0.0155384715 0.0107872879 0.0217786594 0.3476042929 0.0109904917 0.0015919288 0.0071539896 0.0197479052 0.0328352333 0.0009209994 0.0025714024 0.0135302919;
918 frequency C60pi3 = 0.0083680740 0.0007319768 0.0006123446 0.0002228366 0.0020433870 0.0009498685 0.0004731544 0.0004825748 0.0005189995 0.3768453098 0.2608334606 0.0006296168 0.0315700586 0.0123984358 0.0009595916 0.0009746383 0.0049990761 0.0008657759 0.0017132332 0.2938075872;
919 frequency C60pi4 = 0.2227229348 0.0064846074 0.0061206496 0.0007997588 0.1640285908 0.0051051888 0.0027280806 0.0202702520 0.0037183875 0.0455406072 0.0883350071 0.0022832871 0.0348094559 0.0228667054 0.0035471579 0.0850040072 0.1012848285 0.0048424833 0.0096500033 0.1698580069;
920 frequency C60pi5 = 0.0412139519 0.0067627055 0.0051067690 0.0017434391 0.0204715649 0.0057538477 0.0037263409 0.0069107492 0.0180293946 0.1154281623 0.1693562458 0.0042900270 0.0414066566 0.2239001858 0.0058416410 0.0149106129 0.0239548406 0.0332237129 0.1379349474 0.1200342049;
921 frequency C60pi6 = 0.0480550249 0.0308438053 0.0940628721 0.2084606133 0.0037801787 0.0747676701 0.1855184661 0.0191402239 0.0872162350 0.0094685435 0.0277340828 0.0375741243 0.0088308358 0.0196000958 0.0081267777 0.0439680761 0.0324588883 0.0034665720 0.0387499964 0.0181769181;
922 frequency C60pi7 = 0.0062848745 0.0026246919 0.0030342510 0.0005324147 0.0073027627 0.0034409089 0.0009741492 0.0019578159 0.0102225186 0.0180592309 0.1179064681 0.0016205916 0.0234721825 0.3974552519 0.0020165583 0.0056903327 0.0037091821 0.0598639097 0.3185565304 0.0152753744;
923 frequency C60pi8 = 0.1815005560 0.0026845411 0.0148484537 0.0025145485 0.4205633920 0.0014097001 0.0007088144 0.0461854175 0.0014374605 0.0041745536 0.0098310464 0.0006474254 0.0041611385 0.0068976432 0.0038767247 0.1864537050 0.0687189855 0.0027083549 0.0061033012 0.0345742379;
924 frequency C60pi9 = 0.0600740822 0.0367642654 0.0134869242 0.0170572285 0.0070719770 0.0142469806 0.0127486975 0.0343564471 0.0305859029 0.0204571345 0.0994551128 0.0212367087 0.0318165939 0.1140907926 0.0297628218 0.0505792699 0.0339368402 0.2312808862 0.1192491702 0.0217421638;
925 frequency C60pi10 = 0.0708394513 0.0474098489 0.0416822304 0.0324482918 0.0131641265 0.0494874703 0.0508264389 0.0183309196 0.0567272697 0.0650369079 0.1282255556 0.0343618389 0.0390362930 0.0594359563 0.0135608209 0.0551343199 0.0642260358 0.0137118382 0.0673934289 0.0789609573;
926 frequency C60pi11 = 0.0617689371 0.0076332888 0.0303081645 0.3430234188 0.0007199837 0.0307856241 0.3792509407 0.0284658686 0.0079592120 0.0016999627 0.0039945339 0.0216076877 0.0019734329 0.0009814186 0.0174791407 0.0337831940 0.0203426591 0.0006130268 0.0017102752 0.0058992300;
927 frequency C60pi12 = 0.0421559537 0.1042068314 0.0286980872 0.0164385240 0.0044450330 0.1393690851 0.0531949072 0.0134711207 0.0177764997 0.0267727728 0.1967237776 0.1323735242 0.1182827521 0.0086728324 0.0051837880 0.0255852718 0.0333292020 0.0045852327 0.0070281498 0.0217066546;
928 frequency C60pi13 = 0.2814809927 0.0100367066 0.0172867775 0.0064385734 0.0258337508 0.0133101925 0.0115046410 0.0270054934 0.0054629657 0.0188216093 0.0190993462 0.0098712843 0.0158719589 0.0050481705 0.0129510033 0.1886808600 0.2427104979 0.0012274627 0.0036052922 0.0837524211;
929 frequency C60pi14 = 0.2769188320 0.0017226995 0.0021315271 0.0011672545 0.0318292645 0.0018216251 0.0024752467 0.0199646887 0.0005170863 0.0983109006 0.0489264326 0.0016232163 0.0173414948 0.0070843906 0.0070179705 0.0336348952 0.0814141404 0.0007118144 0.0032942319 0.3620922883;
930 frequency C60pi15 = 0.1577797792 0.1112140270 0.0570403237 0.0648290471 0.0053318076 0.1065373681 0.0913586945 0.0906209718 0.0533809635 0.0029171632 0.0156225571 0.0782148712 0.0045758969 0.0025047816 0.0067077844 0.0929310045 0.0393122597 0.0028575821 0.0077590269 0.0085040899;
931 frequency C60pi16 = 0.0593735135 0.0354740772 0.1151175314 0.2189482708 0.0015332173 0.0688752402 0.1819422913 0.0813707101 0.0220478285 0.0020993577 0.0056191259 0.0750172075 0.0021871739 0.0010838321 0.0109737422 0.0726449461 0.0380238271 0.0007346460 0.0026664883 0.0042669729;
932 frequency C60pi17 = 0.0978066326 0.0265576438 0.0101843505 0.0120781428 0.0064138404 0.0307876446 0.0291282947 0.0128912798 0.0128036716 0.0723904209 0.1279438950 0.0245630658 0.0303267312 0.0198963719 0.2723524069 0.0350549441 0.0484557340 0.0046842467 0.0104773833 0.1152032995;
933 frequency C60pi18 = 0.0124023388 0.0030680354 0.0009239105 0.0006037316 0.0041885695 0.0032957441 0.0012524000 0.0011306791 0.0013542104 0.2344167852 0.4550557697 0.0016718177 0.0667307666 0.0610615367 0.0037076169 0.0019420934 0.0067612939 0.0038937184 0.0074911765 0.1290478057;
934 frequency C60pi19 = 0.0794230623 0.1294739355 0.0662792725 0.0587236242 0.0019919499 0.1143880588 0.1246900644 0.0325432311 0.0238605372 0.0036277150 0.0097987961 0.2147597316 0.0041846209 0.0012869951 0.0142410239 0.0615807386 0.0477333594 0.0006525371 0.0029420233 0.0078187231;
935 frequency C60pi20 = 0.0248148778 0.0083552910 0.1888915388 0.4278832998 0.0027839717 0.0210777725 0.1432386297 0.0643968435 0.0185736870 0.0022506941 0.0034558626 0.0179274104 0.0015714503 0.0014680353 0.0073768035 0.0377003132 0.0187767966 0.0005891859 0.0042602708 0.0046072655;
936 frequency C60pi21 = 0.0017003427 0.0060674330 0.0004222900 0.0010711490 0.0029059420 0.0016424179 0.0011731741 0.0035579609 0.0027630465 0.0012291190 0.0127420810 0.0004273804 0.0025671348 0.0513377024 0.0013536738 0.0011871674 0.0014033068 0.8640436936 0.0390912582 0.0033137266;
937 frequency C60pi22 = 0.0468360682 0.0639796924 0.0205603686 0.0185615516 0.0059954138 0.0557030821 0.0705436036 0.0045435329 0.0152062773 0.1550613356 0.0824253382 0.0866248354 0.0245854443 0.0080177192 0.0081485616 0.0237025617 0.0962054496 0.0018368673 0.0067131723 0.2047491243;
938 frequency C60pi23 = 0.0258764792 0.0201097124 0.0298384107 0.0107037437 0.0142503909 0.0158529432 0.0105649532 0.0073064999 0.1411078834 0.0114777629 0.0407992414 0.0119179202 0.0098798997 0.1876429961 0.0051228805 0.0275699644 0.0170764901 0.0405124999 0.3536390834 0.0187502449;
939 frequency C60pi24 = 0.0296285022 0.0046400334 0.0034944393 0.0008851024 0.0090046468 0.0055481111 0.0033046518 0.0027969482 0.0050701500 0.2583397750 0.2668085481 0.0046690936 0.0770825277 0.0408798247 0.0026918193 0.0068538089 0.0322265673 0.0035506055 0.0153353414 0.2271895033;
940 frequency C60pi25 = 0.0555725806 0.0098447861 0.0409064430 0.0140389597 0.0097418602 0.0068727710 0.0069443190 0.0157956555 0.0041631258 0.0069826497 0.0075271247 0.0139224817 0.0058762687 0.0034496730 0.0119733364 0.3482466393 0.4213655981 0.0010061491 0.0026576772 0.0131119012;
941 frequency C60pi26 = 0.0682671212 0.0615207091 0.0530661192 0.0360278709 0.0141433148 0.0612274332 0.0497415394 0.0268696520 0.1127674983 0.0132646615 0.0544493838 0.0482609047 0.0170033964 0.0803375967 0.0191949850 0.0671839752 0.0443995774 0.0199957919 0.1255070748 0.0267713947;
942 frequency C60pi27 = 0.0792618808 0.0638377192 0.0635289371 0.0436646174 0.0049503302 0.0666365188 0.0829639117 0.0183428565 0.0233169239 0.0249427251 0.0221483402 0.0932577596 0.0120893380 0.0049131149 0.0126360122 0.1334848656 0.1916745928 0.0018040086 0.0062353115 0.0503102360;
943 frequency C60pi28 = 0.0731759112 0.2105335985 0.0324200854 0.0110007149 0.0123458504 0.0858951989 0.0349942684 0.0224509173 0.0386903280 0.0246226304 0.0508307349 0.1783344831 0.0185740720 0.0093148787 0.0148722772 0.0603181436 0.0649574934 0.0051046395 0.0130597421 0.0385040321;
944 frequency C60pi29 = 0.0878402710 0.0110331750 0.0060801213 0.0032803903 0.0171147088 0.0109831614 0.0101465790 0.0087090941 0.0054902234 0.1987761871 0.1756460821 0.0082096925 0.0417232903 0.0191954435 0.0111283542 0.0209862621 0.0697718709 0.0031744014 0.0081905473 0.2825201446;
945 frequency C60pi30 = 0.0990215820 0.0349351987 0.0211149501 0.0118797946 0.0108995677 0.0557710676 0.0278999992 0.0240250097 0.0123445071 0.0776564721 0.2354511299 0.0322817789 0.1207665429 0.0214442058 0.0075655541 0.0524170141 0.0649785115 0.0047075806 0.0077328724 0.0771066610;
946 frequency C60pi31 = 0.0601641168 0.0161995226 0.2783522747 0.0337188808 0.0315066987 0.0210645987 0.0059839451 0.0543080710 0.0531523512 0.0070650825 0.0070698142 0.0139598368 0.0088298653 0.0069525877 0.0075834331 0.2829802556 0.0860317092 0.0014966551 0.0134849454 0.0100953553;
947 frequency C60pi32 = 0.0049781737 0.0018412331 0.0007012207 0.0005315368 0.0052978737 0.0024089907 0.0007630546 0.0015051317 0.0041575221 0.0443828633 0.4417417476 0.0011615060 0.0602807417 0.3351117140 0.0027847686 0.0025795769 0.0030288544 0.0171302592 0.0458455751 0.0237676560;
948 frequency C60pi33 = 0.0251996593 0.1114468110 0.0142031925 0.0041012288 0.0097099500 0.0620070749 0.0262571641 0.0038067269 0.0431938935 0.0974043253 0.2447197423 0.0824312856 0.0539323021 0.0429091639 0.0052658505 0.0096093107 0.0251183002 0.0146571900 0.0456965140 0.0783303143;
949 frequency C60pi34 = 0.0230361648 0.0014748749 0.0013534390 0.0006264439 0.0048580122 0.0009870046 0.0015762583 0.0011565336 0.0008899238 0.3952895890 0.0576537208 0.0014663528 0.0140986541 0.0072127040 0.0020177885 0.0028770237 0.0205580852 0.0005477695 0.0019539080 0.4603657493;
950 frequency C60pi35 = 0.1408776963 0.0297808449 0.0171297613 0.0285076933 0.0032213718 0.0320632225 0.0423838922 0.0299558472 0.0131321477 0.0066914481 0.0195120028 0.0383781635 0.0036276863 0.0041231064 0.4383466229 0.0851400095 0.0422765692 0.0013236871 0.0037087638 0.0198194632;
951 frequency C60pi36 = 0.4442491220 0.0050216551 0.0102305117 0.0057193038 0.0235405374 0.0055997640 0.0064889886 0.0822687710 0.0025505743 0.0033615104 0.0040990063 0.0038097073 0.0028683069 0.0024413211 0.0162890960 0.2999969708 0.0559664935 0.0007735426 0.0020639824 0.0226608347;
952 frequency C60pi37 = 0.0898717958 0.0070958305 0.0130067619 0.0129166888 0.0044131479 0.0023806547 0.0058957027 0.8087563021 0.0016517855 0.0004339282 0.0015564455 0.0033939025 0.0004253422 0.0008073572 0.0034128140 0.0362876891 0.0032887534 0.0015223902 0.0008537454 0.0020289624;
953 frequency C60pi38 = 0.0550840246 0.0472254260 0.1877829604 0.1273796123 0.0035824944 0.0527969268 0.0655884730 0.0637607521 0.0404883483 0.0075574152 0.0136304510 0.0867682792 0.0081684229 0.0040375032 0.0110681809 0.1263380956 0.0752544318 0.0013563681 0.0118590434 0.0102727908;
954 frequency C60pi39 = 0.0117681394 0.0442558806 0.0844144627 0.0144712108 0.0070388254 0.1038342049 0.0110901161 0.0049626578 0.4337194047 0.0061337038 0.0298794939 0.0137928558 0.0076237551 0.0338266335 0.0081346096 0.0140571089 0.0108276801 0.0080683065 0.1437251732 0.0083757773;
955 frequency C60pi40 = 0.0159285638 0.0048098656 0.0032692643 0.0010966937 0.0080519916 0.0134552459 0.0021324215 0.0025086365 0.0049192147 0.0501543893 0.5307634291 0.0035599431 0.2160085187 0.0743650717 0.0045247350 0.0066922196 0.0119092283 0.0070928134 0.0106565111 0.0281012433;
956 frequency C60pi41 = 0.0195973253 0.0105142992 0.3289103336 0.3099848991 0.0034539049 0.0116196758 0.0250777800 0.0627528956 0.0295961112 0.0032650434 0.0028246884 0.0240963907 0.0008425062 0.0019706550 0.0049062781 0.1064984500 0.0438053705 0.0006333959 0.0056197958 0.0040302013;
957 frequency C60pi42 = 0.0833804360 0.0125871438 0.0969824220 0.0686820704 0.0081981143 0.0121520930 0.0227415415 0.0982291876 0.0073954898 0.0017471177 0.0039653113 0.0129342146 0.0019557975 0.0024132583 0.0355924232 0.3115606483 0.2113368612 0.0016329034 0.0017991083 0.0047138579;
958 frequency C60pi43 = 0.0181409133 0.4129662563 0.0233205154 0.0033333547 0.0085143598 0.0526694251 0.0096531879 0.0224552642 0.0375238929 0.0035090482 0.0149146621 0.3208065790 0.0046098856 0.0035426859 0.0087197469 0.0262309419 0.0131791136 0.0034766995 0.0079588201 0.0044746474;
959 frequency C60pi44 = 0.2494227404 0.0185481724 0.0164119567 0.0169234299 0.0122862654 0.0228501981 0.0370491083 0.0347467705 0.0087069587 0.0595718359 0.0451065029 0.0177064733 0.0204556127 0.0077360919 0.0686403544 0.0889295672 0.0986017356 0.0028603862 0.0061938477 0.1672519917;
960 frequency C60pi45 = 0.1419737638 0.0373945961 0.0576296888 0.0537452477 0.0068856658 0.0286239972 0.0407540287 0.3988107872 0.0152895617 0.0016627616 0.0092348297 0.0314273807 0.0055425500 0.0040286132 0.0180328866 0.1123731997 0.0242478202 0.0025909098 0.0049054208 0.0048462908;
961 frequency C60pi46 = 0.0178903305 0.1958843646 0.0155853897 0.0031054277 0.0290304227 0.1051819261 0.0040503389 0.0100480293 0.1252696215 0.0016708003 0.0722356645 0.0233340169 0.0116142354 0.0238913260 0.0009938415 0.0181675536 0.0186260222 0.2260554691 0.0859787232 0.0113864962;
962 frequency C60pi47 = 0.1454758367 0.0420979067 0.0400419720 0.1294249748 0.0014186329 0.0906469055 0.2471353458 0.0319650773 0.0130426183 0.0058525371 0.0123593139 0.0818154090 0.0044178939 0.0017552077 0.0151135525 0.0656688174 0.0511289472 0.0007731441 0.0029258438 0.0169400635;
963 frequency C60pi48 = 0.0169799462 0.0242346701 0.1318047919 0.1043655101 0.0022087215 0.0269349684 0.0376379591 0.5404470183 0.0181137053 0.0007459679 0.0021146994 0.0508617611 0.0009473769 0.0006780593 0.0038754401 0.0297030159 0.0045836180 0.0006031889 0.0015704090 0.0015891728;
964 frequency C60pi49 = 0.0402646249 0.1152022601 0.0323829165 0.0293968352 0.0039388655 0.2497008043 0.1603524245 0.0129260411 0.0617967839 0.0098491259 0.0354918823 0.1448804422 0.0124818865 0.0041153375 0.0043374229 0.0243246958 0.0305645368 0.0026676598 0.0097227847 0.0156026694;
965 frequency C60pi50 = 0.2256914610 0.0523417493 0.0244308734 0.0637125217 0.0043390149 0.0578159236 0.1154830640 0.0867335173 0.0131066949 0.0085086217 0.0193314218 0.0660468804 0.0064877206 0.0027440054 0.0611149102 0.1070877179 0.0507677144 0.0013695913 0.0028982948 0.0299883012;
966 frequency C60pi51 = 0.0033164209 0.0015310773 0.0030830171 0.0008266472 0.0051890730 0.0011024889 0.0005134130 0.0010432830 0.0278451262 0.0041895268 0.0111212494 0.0007149922 0.0023621780 0.3801761447 0.0008365077 0.0035876698 0.0023608948 0.0333346985 0.5107889643 0.0060766272;
967 frequency C60pi52 = 0.1995014012 0.0236078675 0.0392254543 0.0094955104 0.0584590451 0.0254265363 0.0125535371 0.0939787338 0.0341857201 0.0140209879 0.0449387571 0.0118723304 0.0246990633 0.0634433944 0.0145385320 0.1663920640 0.0533159207 0.0129802666 0.0606346163 0.0367302614;
968 frequency C60pi53 = 0.0319448994 0.1011667268 0.2084709220 0.0378074649 0.0066040348 0.0766372935 0.0279488190 0.0365541130 0.2088643258 0.0047542347 0.0156545731 0.0868664783 0.0043253317 0.0108915768 0.0060899575 0.0577656939 0.0302051160 0.0026001883 0.0387897304 0.0060585202;
969 frequency C60pi54 = 0.0776799515 0.0142518583 0.0403216692 0.0080651725 0.0140092962 0.0179995517 0.0112622427 0.0136868237 0.0133729897 0.1239635380 0.0724670993 0.0129144967 0.0420745442 0.0173584908 0.0117084432 0.0922723571 0.2316899445 0.0028153633 0.0141726542 0.1679135132;
970 frequency C60pi55 = 0.1183662657 0.0805192606 0.0259524932 0.0495595439 0.0035624835 0.1204924917 0.1537589210 0.0194993426 0.0229373171 0.0302661211 0.0571250629 0.0982304112 0.0171727472 0.0068665705 0.0175153030 0.0486588400 0.0635796210 0.0023008307 0.0083027431 0.0553336300;
971 frequency C60pi56 = 0.0528559899 0.0193569043 0.0264743774 0.2092761515 0.0008625883 0.1212409715 0.4024189781 0.0155838458 0.0124148798 0.0054864832 0.0090256472 0.0497017031 0.0042357114 0.0012650715 0.0063185636 0.0197262901 0.0235463735 0.0008381610 0.0033948741 0.0159764347;
972 frequency C60pi57 = 0.0344366215 0.0426221820 0.1636716191 0.1139007491 0.0020985982 0.0605413987 0.0541780220 0.3361639671 0.0461776737 0.0003463416 0.0048355678 0.0667552967 0.0019704509 0.0031557619 0.0040369775 0.0481173332 0.0089148085 0.0006510101 0.0054145649 0.0020110555;
973 frequency C60pi58 = 0.1153088951 0.0151278638 0.0458476603 0.1755516676 0.0014962362 0.0366731222 0.1749410045 0.0394181311 0.0132401530 0.0056912974 0.0101409559 0.0433118387 0.0030332064 0.0015700232 0.1665802563 0.0871536033 0.0468260603 0.0007515702 0.0031432715 0.0141931831;
974 frequency C60pi59 = 0.3865149348 0.0037579334 0.0030420497 0.0022366810 0.0218928357 0.0021464743 0.0031387843 0.3694353983 0.0014672902 0.0085376076 0.0127257242 0.0018840458 0.0080581695 0.0039281367 0.0158688291 0.0808877279 0.0305195935 0.0009922880 0.0019020345 0.0410634615;
975 frequency C60pi60 = 0.0146570745 0.0028841333 0.0012998335 0.0005210575 0.0024317913 0.0049362750 0.0014874369 0.0020953252 0.0010181940 0.1913901476 0.4432797758 0.0022898369 0.2217427062 0.0091637503 0.0007685153 0.0027251487 0.0170997497 0.0008779380 0.0014756028 0.0778557075;
976 model C60 = POISSON+G+FMIX{C60pi1:1:0.0169698865,C60pi2:1:0.0211683374,C60pi3:1:0.0276589079,C60pi4:1:0.0065675964,C60pi5:1:0.0141221416,C60pi6:1:0.0068774834,C60pi7:1:0.0146909701,C60pi8:1:0.0067225777,C60pi9:1:0.0018396660,C60pi10:1:0.0102547197,C60pi11:1:0.0230896163,C60pi12:1:0.0057941033,C60pi13:1:0.0125394534,C60pi14:1:0.0204526478,C60pi15:1:0.0070629602,C60pi16:1:0.0117982741,C60pi17:1:0.0068334668,C60pi18:1:0.0433775839,C60pi19:1:0.0318278731,C60pi20:1:0.0222546108,C60pi21:1:0.0102264969,C60pi22:1:0.0150545891,C60pi23:1:0.0134159878,C60pi24:1:0.0148552065,C60pi25:1:0.0239111516,C60pi26:1:0.0128776278,C60pi27:1:0.0222318842,C60pi28:1:0.0247444742,C60pi29:1:0.0214274810,C60pi30:1:0.0115001882,C60pi31:1:0.0076017389,C60pi32:1:0.0130258568,C60pi33:1:0.0093701965,C60pi34:1:0.0467194264,C60pi35:1:0.0441940314,C60pi36:1:0.0322263154,C60pi37:1:0.0402999891,C60pi38:1:0.0150234227,C60pi39:1:0.0104589903,C60pi40:1:0.0214742395,C60pi41:1:0.0154957836,C60pi42:1:0.0101789953,C60pi43:1:0.0227980379,C60pi44:1:0.0123204539,C60pi45:1:0.0066777583,C60pi46:1:0.0004150083,C60pi47:1:0.0344385130,C60pi48:1:0.0113663379,C60pi49:1:0.0127143049,C60pi50:1:0.0124323741,C60pi51:1:0.0262124415,C60pi52:1:0.0064994957,C60pi53:1:0.0103203293,C60pi54:1:0.0142463512,C60pi55:1:0.0215600067,C60pi56:1:0.0199150700,C60pi57:1:0.0038964200,C60pi58:1:0.0113448855,C60pi59:1:0.0128595846,C60pi60:1:0.0117656776};
977
978 end;
979 )";
980
981 const double MIN_MIXTURE_PROP = 0.001;
982 //const double MAX_MIXTURE_PROP = 1000.0;
983 //const double MIN_MIXTURE_RATE = 0.01;
984 //const double MAX_MIXTURE_RATE = 100.0;
985
createModel(string model_str,ModelsBlock * models_block,StateFreqType freq_type,string freq_params,PhyloTree * tree)986 ModelSubst* createModel(string model_str, ModelsBlock *models_block, StateFreqType freq_type, string freq_params,
987 PhyloTree* tree)
988 {
989 ModelSubst *model = NULL;
990 //cout << "Numstates: " << tree->aln->num_states << endl;
991 string model_params;
992 NxsModel *nxsmodel = models_block->findModel(model_str);
993 if (nxsmodel) model_params = nxsmodel->description;
994
995 // PoMo.
996 bool pomo = false;
997 string pomo_rate_str = "";
998 string pomo_heterozygosity = "";
999 string::size_type p_pos = posPOMO(model_str);
1000 pomo = (p_pos != string::npos);
1001
1002 if (pomo) {
1003 if (model_str[p_pos+2] == '{') {
1004 string::size_type close_bracket = model_str.find("}", p_pos);
1005 if (close_bracket == string::npos) {
1006 cout << "Model string: " << model_str << endl;
1007 outError("No closing bracket in PoMo parameters.");
1008 }
1009 else {
1010 pomo_heterozygosity = model_str.substr(p_pos+3,close_bracket-p_pos-3);
1011 model_str = model_str.substr(0, p_pos) + model_str.substr(close_bracket+1);
1012 }
1013 }
1014 else {
1015 model_str = model_str.substr(0, p_pos) + model_str.substr(p_pos + 2);
1016 }
1017
1018 size_t pomo_rate_start_pos;
1019 if ((pomo_rate_start_pos = model_str.find("+G")) != string::npos) {
1020 size_t pomo_rate_end_pos = model_str.find_first_of("+*", pomo_rate_start_pos+1);
1021 if (pomo_rate_end_pos == string::npos) {
1022 pomo_rate_str = model_str.substr(pomo_rate_start_pos, model_str.length() - pomo_rate_start_pos);
1023 model_str = model_str.substr(0, pomo_rate_start_pos);
1024 } else {
1025 pomo_rate_str = model_str.substr(pomo_rate_start_pos, pomo_rate_end_pos - pomo_rate_start_pos);
1026 model_str = model_str.substr(0, pomo_rate_start_pos) + model_str.substr(pomo_rate_end_pos);
1027 }
1028 }
1029 }
1030
1031 // Now that PoMo stuff has been removed, check for model parameters.
1032 size_t pos = model_str.find(OPEN_BRACKET);
1033 if (pos != string::npos) {
1034 if (model_str.rfind(CLOSE_BRACKET) != model_str.length()-1)
1035 outError("Close bracket not found at the end of ", model_str);
1036 model_params = model_str.substr(pos+1, model_str.length()-pos-2);
1037 model_str = model_str.substr(0, pos);
1038 }
1039
1040 /*
1041 if ((model_str == "JC" && tree->aln->seq_type == SEQ_DNA) ||
1042 (model_str == "POISSON" && tree->aln->seq_type == SEQ_PROTEIN) ||
1043 (model_str == "JC2" && tree->aln->seq_type == SEQ_BINARY) ||
1044 (model_str == "JCC" && tree->aln->seq_type == SEQ_CODON) ||
1045 (model_str == "MK" && tree->aln->seq_type == SEQ_MORPH))
1046 {
1047 model = new ModelSubst(tree->aln->num_states);
1048 } else */
1049
1050 if ((pomo) || (tree->aln->seq_type == SEQ_POMO)) {
1051 if (pomo_rate_str == "")
1052 model = new ModelPoMo(model_str.c_str(), model_params, freq_type, freq_params, tree, pomo_heterozygosity);
1053 else
1054 model = new ModelPoMoMixture(model_str.c_str(), model_params, freq_type, freq_params, tree, pomo_heterozygosity, pomo_rate_str);
1055 if (model->isMixture() && verbose_mode >= VB_MED)
1056 cout << "PoMo mixture model for Gamma rate heterogeneity." << endl;
1057 // else if ((model_str == "GTR" && tree->aln->seq_type == SEQ_DNA) ||
1058 // (model_str == "GTR2" && tree->aln->seq_type == SEQ_BINARY) ||
1059 // (model_str == "GTR20" && tree->aln->seq_type == SEQ_PROTEIN)) {
1060 // model = new ModelGTR(tree, count_rates);
1061 // if (freq_params != "")
1062 // ((ModelGTR*)model)->readStateFreq(freq_params);
1063 // if (model_params != "")
1064 // ((ModelGTR*)model)->readRates(model_params);
1065 // ((ModelGTR*)model)->init(freq_type);
1066 // } else
1067 } else if (ModelMarkov::validModelName(model_str)) {
1068 model = ModelMarkov::getModelByName(model_str, tree, model_params, freq_type, freq_params);
1069 } else if (tree->aln->seq_type == SEQ_BINARY) {
1070 model = new ModelBIN(model_str.c_str(), model_params, freq_type, freq_params, tree);
1071 } else if (tree->aln->seq_type == SEQ_DNA) {
1072 model = new ModelDNA(model_str.c_str(), model_params, freq_type, freq_params, tree);
1073 } else if (tree->aln->seq_type == SEQ_PROTEIN) {
1074 model = new ModelProtein(model_str.c_str(), model_params, freq_type, freq_params, tree, models_block);
1075 } else if (tree->aln->seq_type == SEQ_CODON) {
1076 model = new ModelCodon(model_str.c_str(), model_params, freq_type, freq_params, tree);
1077 } else if (tree->aln->seq_type == SEQ_MORPH) {
1078 model = new ModelMorphology(model_str.c_str(), model_params, freq_type, freq_params, tree);
1079 } else {
1080 outError("Unsupported model type");
1081 }
1082
1083 return model;
1084 }
1085
1086 /**
1087 constructor
1088 @param tree associated tree for the model
1089 */
ModelMixture(PhyloTree * tree)1090 ModelMixture::ModelMixture(PhyloTree *tree) : ModelMarkov(tree) {
1091 prop = NULL;
1092 fix_prop = true;
1093 optimizing_submodels = false;
1094 }
1095
ModelMixture(string orig_model_name,string model_name,string model_list,ModelsBlock * models_block,StateFreqType freq,string freq_params,PhyloTree * tree,bool optimize_weights)1096 ModelMixture::ModelMixture(string orig_model_name, string model_name, string model_list, ModelsBlock *models_block,
1097 StateFreqType freq, string freq_params, PhyloTree *tree, bool optimize_weights)
1098 : ModelMarkov(tree)
1099 {
1100 prop = NULL;
1101 fix_prop = true;
1102 optimizing_submodels = false;
1103 optimize_steps = 0;
1104 initMixture(orig_model_name, model_name, model_list, models_block, freq, freq_params, tree, optimize_weights);
1105 }
1106
initMixture(string orig_model_name,string model_name,string model_list,ModelsBlock * models_block,StateFreqType freq,string freq_params,PhyloTree * tree,bool optimize_weights)1107 void ModelMixture::initMixture(string orig_model_name, string model_name, string model_list, ModelsBlock *models_block,
1108 StateFreqType freq, string freq_params, PhyloTree *tree, bool optimize_weights)
1109 {
1110 // const int MAX_MODELS = 64;
1111 size_t cur_pos;
1112 int m;
1113
1114 NxsModel *nxs_freq_empirical = new NxsModel("empirical");
1115 NxsModel *nxs_freq_optimize = new NxsModel("optimize");
1116
1117 int num_pre_freq = 0;
1118
1119 vector<NxsModel*> freq_vec;
1120 DoubleVector freq_rates;
1121 DoubleVector freq_weights;
1122 fix_prop = false;
1123 optimizing_submodels = false;
1124
1125 if (freq == FREQ_MIXTURE) {
1126 for (m = 0, cur_pos = 0; cur_pos < freq_params.length(); m++) {
1127 size_t pos = freq_params.find(',', cur_pos);
1128 if (pos == string::npos)
1129 pos = freq_params.length();
1130 if (pos <= cur_pos)
1131 outError("One frequency name in the mixture is empty.");
1132 string this_name = freq_params.substr(cur_pos, pos-cur_pos);
1133 double rate = 1.0, weight = 1.0;
1134 size_t pos_rate = this_name.find(':');
1135 if (pos_rate != string::npos) {
1136 size_t pos_weight = this_name.find(':', pos_rate+1);
1137 if (pos_weight == string::npos) {
1138 rate = convert_double(this_name.substr(pos_rate+1).c_str());
1139 } else {
1140 rate = convert_double(this_name.substr(pos_rate+1, pos_weight-pos_rate-1).c_str());
1141 weight = convert_double(this_name.substr(pos_weight+1).c_str());
1142 fix_prop = true;
1143 if (weight <= 0.0)
1144 outError("Mixture component weight is negative!");
1145 weight = max(weight, MIN_MIXTURE_PROP);
1146 }
1147 this_name = this_name.substr(0, pos_rate);
1148 }
1149 freq_rates.push_back(rate);
1150 freq_weights.push_back(weight);
1151 cur_pos = pos+1;
1152 if (this_name == nxs_freq_empirical->name) {
1153 freq_vec.push_back(nxs_freq_empirical);
1154 num_pre_freq++;
1155 } else if (this_name == nxs_freq_optimize->name) {
1156 freq_vec.push_back(nxs_freq_optimize);
1157 num_pre_freq++;
1158 } else {
1159 NxsModel *freq_mod = models_block->findModel(this_name);
1160 if (!freq_mod)
1161 outError("Frequency mixture name not found ", this_name);
1162 if (!(freq_mod->flag & NM_FREQ)) {
1163 cout << freq_mod->flag << endl;
1164 outError("Frequency mixture name does not corresponding to frequency model ", this_name);
1165 }
1166 freq_vec.push_back(freq_mod);
1167 }
1168 if (num_pre_freq >= 2)
1169 outError("Defining both empirical and optimize frequencies not allowed");
1170 }
1171 double sum_weights = 0.0;
1172 for (m = 0; m < freq_weights.size(); m++)
1173 if (freq_vec[m] != nxs_freq_empirical && freq_vec[m] != nxs_freq_optimize)
1174 sum_weights += freq_weights[m];
1175 for (m = 0; m < freq_weights.size(); m++)
1176 if (freq_vec[m] == nxs_freq_empirical || freq_vec[m] == nxs_freq_optimize)
1177 freq_weights[m] = sum_weights/freq_weights.size();
1178 ModelMarkov::init(FREQ_USER_DEFINED);
1179 } else {
1180 if (freq_params != "")
1181 readStateFreq(freq_params);
1182 if (freq == FREQ_UNKNOWN)
1183 freq = FREQ_USER_DEFINED;
1184 ModelMarkov::init(freq);
1185 }
1186
1187 DoubleVector weights;
1188 name = orig_model_name.substr(0, orig_model_name.find_first_of("+*"));
1189 if (!models_block->findMixModel(name))
1190 name = "";
1191 full_name = (string)"MIX" + OPEN_BRACKET;
1192 if (model_list == "") model_list = model_name;
1193 for (m = 0, cur_pos = 0; cur_pos < model_list.length(); m++) {
1194 size_t pos = model_list.find(',', cur_pos);
1195 if (pos == string::npos)
1196 pos = model_list.length();
1197 if (pos <= cur_pos)
1198 outError("One model name in the mixture is empty.");
1199 string this_name = model_list.substr(cur_pos, pos-cur_pos);
1200 double rate = 1.0, weight = 1.0;
1201 size_t pos_rate = this_name.find(':');
1202 if (pos_rate != string::npos) {
1203 size_t pos_weight = this_name.find(':', pos_rate+1);
1204 if (pos_weight == string::npos) {
1205 rate = convert_double(this_name.substr(pos_rate+1).c_str());
1206 } else {
1207 rate = convert_double(this_name.substr(pos_rate+1, pos_weight-pos_rate-1).c_str());
1208 weight = convert_double(this_name.substr(pos_weight+1).c_str());
1209 fix_prop = true;
1210 if (weight <= 0.0)
1211 outError("Mixture component weight is negative!");
1212 }
1213 this_name = this_name.substr(0, pos_rate);
1214 }
1215 cur_pos = pos+1;
1216 ModelMarkov* model;
1217 if (freq == FREQ_MIXTURE) {
1218 for(int f = 0; f != freq_vec.size(); f++) {
1219 if (freq_vec[f] == nxs_freq_empirical)
1220 model = (ModelMarkov*)createModel(this_name, models_block, FREQ_EMPIRICAL, "", tree);
1221 else if (freq_vec[f] == nxs_freq_optimize)
1222 model = (ModelMarkov*)createModel(this_name, models_block, FREQ_ESTIMATE, "", tree);
1223 else
1224 model = (ModelMarkov*)createModel(this_name, models_block, FREQ_USER_DEFINED, freq_vec[f]->description, tree);
1225 model->total_num_subst = rate * freq_rates[f];
1226 push_back(model);
1227 weights.push_back(weight * freq_weights[f]);
1228 if (m+f > 0) {
1229 // name += ',';
1230 full_name += ',';
1231 }
1232 if (freq_vec[f] == nxs_freq_empirical) {
1233 model->name += "+F";
1234 model->full_name += "+F";
1235 } else if (freq_vec[f] == nxs_freq_optimize) {
1236 model->name += "+FO";
1237 model->full_name += "+FO";
1238 } else {
1239 model->name += "+F" +freq_vec[f]->name + "";
1240 model->full_name += "+F" +freq_vec[f]->name + "";
1241 }
1242 // name += model->name;
1243 full_name += model->name;
1244 }
1245 } else {
1246 model = (ModelMarkov*)createModel(this_name, models_block, freq, freq_params, tree);
1247 model->total_num_subst = rate;
1248 push_back(model);
1249 weights.push_back(weight);
1250 if (m > 0) {
1251 // name += ',';
1252 full_name += ',';
1253 }
1254 // name += model->name;
1255 full_name += model->name;
1256 }
1257 }
1258
1259 // name += CLOSE_BRACKET;
1260 full_name += CLOSE_BRACKET;
1261
1262 int nmixtures = size();
1263 if (prop)
1264 aligned_free(prop);
1265 prop = aligned_alloc<double>(nmixtures);
1266
1267 double sum = 0.0;
1268 int i;
1269 if (fix_prop) {
1270 for (i = 0, sum = 0.0; i < nmixtures; i++) {
1271 prop[i] = weights[i];
1272 sum += prop[i];
1273 }
1274 } else {
1275 // initialize rates as increasing
1276 for (i = 0, sum = 0.0; i < nmixtures; i++) {
1277 // prop[i] = random_double();
1278 prop[i] = 1.0/nmixtures;
1279 sum += prop[i];
1280 }
1281 }
1282 // normalize weights to 1.0
1283 if (sum != 1.0) {
1284 sum = 1.0/sum;
1285 // cout << "NOTE: Mixture weights do not sum up to 1, rescale weights by " << sum << endl;
1286 for (i = 0; i < nmixtures; i++)
1287 prop[i] *= sum;
1288 }
1289
1290 // rescale total_num_subst such that the global rate is 1
1291 for (i = 0, sum = 0.0; i < nmixtures; i++)
1292 sum += prop[i]*at(i)->total_num_subst;
1293 for (i = 0; i < nmixtures; i++)
1294 at(i)->total_num_subst /= sum;
1295
1296 if (optimize_steps == 0)
1297 optimize_steps = (getNDim()+1)*100;
1298
1299 if (optimize_weights) fix_prop = false;
1300 fix_prop |= (nmixtures == 1);
1301 // use central eigen etc. stufffs
1302
1303 // check reversibility
1304 bool rev = front()->isReversible();
1305 bool err = false;
1306 for (i = 1; i < nmixtures; i++) {
1307 if (at(i)->isReversible() != rev) {
1308 cerr << "ERROR: Model " << at(i)->name << " has different reversible property" << endl;
1309 err = true;
1310 }
1311 }
1312
1313 if (err)
1314 outError("Model reversibility is not consistent");
1315 if (rev != isReversible())
1316 setReversible(rev);
1317
1318 // forgot to call this after refactoring
1319 if (isReversible())
1320 initMem();
1321
1322 decomposeRateMatrix();
1323
1324 delete nxs_freq_optimize;
1325 delete nxs_freq_empirical;
1326
1327 }
1328
initMem()1329 void ModelMixture::initMem() {
1330
1331 int nmixtures = size();
1332
1333 // Calculate the total number of states and take into account that each of the
1334 // models may be a mixture model itself (PoMo rate heterogeneity).
1335
1336 int num_states_total = 0;
1337 for (iterator it = begin(); it != end(); it++)
1338 num_states_total += (*it)->get_num_states_total();
1339
1340 if (eigenvalues) aligned_free(eigenvalues);
1341 if (eigenvectors) aligned_free(eigenvectors);
1342 if (inv_eigenvectors) aligned_free(inv_eigenvectors);
1343 // if (eigen_coeff) aligned_free(eigen_coeff);
1344
1345 eigenvalues = aligned_alloc<double>(num_states_total*nmixtures);
1346 eigenvectors = aligned_alloc<double>(num_states_total*num_states_total*nmixtures);
1347 inv_eigenvectors = aligned_alloc<double>(num_states_total*num_states_total*nmixtures);
1348 // int ncoeff = num_states_total*num_states_total*num_states_total;
1349 // eigen_coeff = aligned_alloc<double>(ncoeff*nmixtures);
1350
1351 // assigning memory for individual models
1352 int m = 0;
1353 int count_num_states = 0;
1354 int count_num_states_2 = 0;
1355 for (iterator it = begin(); it != end(); it++, m++) {
1356 int num_states_this_model = (*it)->get_num_states_total();
1357 int num_states_this_model_2 = num_states_this_model * num_states_this_model;
1358 // first copy memory for eigen stuffs
1359 memcpy(&eigenvalues[count_num_states], (*it)->eigenvalues,
1360 num_states_this_model*sizeof(double));
1361 memcpy(&eigenvectors[count_num_states_2], (*it)->eigenvectors,
1362 num_states_this_model_2*sizeof(double));
1363 memcpy(&inv_eigenvectors[count_num_states_2], (*it)->inv_eigenvectors,
1364 num_states_this_model_2*sizeof(double));
1365 // memcpy(&eigen_coeff[m*ncoeff], (*it)->eigen_coeff, ncoeff*sizeof(double));
1366
1367 // then delete
1368 if ((*it)->eigenvalues) aligned_free((*it)->eigenvalues);
1369 if ((*it)->eigenvectors) aligned_free((*it)->eigenvectors);
1370 if ((*it)->inv_eigenvectors) aligned_free((*it)->inv_eigenvectors);
1371 // if ((*it)->eigen_coeff) aligned_free((*it)->eigen_coeff);
1372
1373 // And assign new memory. Also, recursively, update respective pointers for
1374 // the mixture components of the current model. This is relevant if the
1375 // current model is a mixture model itself.
1376 (*it)->update_eigen_pointers(&eigenvalues[count_num_states],
1377 &eigenvectors[count_num_states_2],
1378 &inv_eigenvectors[count_num_states_2]);
1379 // (*it)->eigen_coeff = &eigen_coeff[m*ncoeff];
1380
1381 // Update the state counters, so that the pointers are assigned correctly
1382 // for the next mixture component.
1383 count_num_states += num_states_this_model;
1384 count_num_states_2 += num_states_this_model_2;
1385 }
1386 }
1387
~ModelMixture()1388 ModelMixture::~ModelMixture() {
1389 if (prop)
1390 aligned_free(prop);
1391 for (reverse_iterator rit = rbegin(); rit != rend(); rit++) {
1392 // (*rit)->eigen_coeff = NULL;
1393 (*rit)->eigenvalues = NULL;
1394 (*rit)->eigenvectors = NULL;
1395 (*rit)->inv_eigenvectors = NULL;
1396 delete (*rit);
1397 }
1398 }
1399
setCheckpoint(Checkpoint * checkpoint)1400 void ModelMixture::setCheckpoint(Checkpoint *checkpoint) {
1401 CheckpointFactory::setCheckpoint(checkpoint);
1402 for (iterator it = begin(); it != end(); it++)
1403 (*it)->setCheckpoint(checkpoint);
1404 }
1405
startCheckpoint()1406 void ModelMixture::startCheckpoint() {
1407 checkpoint->startStruct("ModelMixture" + convertIntToString(getNMixtures()));
1408 }
1409
saveCheckpoint()1410 void ModelMixture::saveCheckpoint() {
1411 startCheckpoint();
1412 // CKP_SAVE(fix_prop);
1413 if (!fix_prop) {
1414 int nmix = getNMixtures();
1415 CKP_ARRAY_SAVE(nmix, prop);
1416 }
1417 int part = 1;
1418 for (iterator it = begin(); it != end(); it++, part++) {
1419 checkpoint->startStruct("Component" + convertIntToString(part));
1420 (*it)->saveCheckpoint();
1421 checkpoint->endStruct();
1422 }
1423 endCheckpoint();
1424
1425 // ModelMarkov::saveCheckpoint();
1426 }
1427
restoreCheckpoint()1428 void ModelMixture::restoreCheckpoint() {
1429 // ModelMarkov::restoreCheckpoint();
1430
1431 startCheckpoint();
1432 // CKP_RESTORE(fix_prop);
1433 if (!fix_prop) {
1434 int nmix = getNMixtures();
1435 CKP_ARRAY_RESTORE(nmix, prop);
1436 }
1437 int part = 1;
1438 for (iterator it = begin(); it != end(); it++, part++) {
1439 checkpoint->startStruct("Component" + convertIntToString(part));
1440 (*it)->restoreCheckpoint();
1441 checkpoint->endStruct();
1442 }
1443 endCheckpoint();
1444
1445 decomposeRateMatrix();
1446 if (phylo_tree)
1447 phylo_tree->clearAllPartialLH();
1448 }
1449
getStateFrequency(double * state_freq,int mixture)1450 void ModelMixture::getStateFrequency(double *state_freq, int mixture) {
1451 ASSERT(mixture < getNMixtures());
1452 if (mixture >= 0) {
1453 at(mixture)->getStateFrequency(state_freq);
1454 return;
1455 }
1456 // special case: return weighted sum of state_freq across classes
1457 // for mixture model, take the weighted sum of frequency vectors
1458 double state_freq_class[num_states];
1459 int mix = getNMixtures();
1460 memset(state_freq, 0, sizeof(double)*num_states);
1461 bool fused = isFused();
1462 for (int i = 0; i < mix; i++) {
1463 at(i)->getStateFrequency(state_freq_class);
1464 double weight = getMixtureWeight(i);
1465 // fused model, take the weight from site_rate
1466 if (fused)
1467 weight = phylo_tree->getRate()->getProp(i) / (1.0 - phylo_tree->getRate()->getPInvar());
1468 for (int j = 0; j < num_states; j++)
1469 state_freq[j] += weight*state_freq_class[j];
1470 }
1471 // // DEBUG.
1472 // cout << "Weighted state frequency of mixture component zero: ";
1473 // for (int i = 0; i < num_states; i++) {
1474 // cout << state_freq[i] << " ";
1475 // }
1476 // cout << endl;
1477 }
1478
computeTransMatrix(double time,double * trans_matrix,int mixture)1479 void ModelMixture::computeTransMatrix(double time, double *trans_matrix, int mixture) {
1480 ASSERT(mixture < getNMixtures());
1481 at(mixture)->computeTransMatrix(time, trans_matrix);
1482 }
1483
computeTransDerv(double time,double * trans_matrix,double * trans_derv1,double * trans_derv2,int mixture)1484 void ModelMixture::computeTransDerv(double time, double *trans_matrix,
1485 double *trans_derv1, double *trans_derv2, int mixture) {
1486 ASSERT(mixture < getNMixtures());
1487 at(mixture)->computeTransDerv(time, trans_matrix, trans_derv1, trans_derv2);
1488 }
1489
getNDim()1490 int ModelMixture::getNDim() {
1491 // int dim = (fix_prop) ? 0: (size()-1);
1492 int dim = 0;
1493 if (!optimizing_submodels && !fix_prop)
1494 dim = size()-1;
1495 for (iterator it = begin(); it != end(); it++)
1496 dim += (*it)->getNDim();
1497 return dim;
1498 }
1499
getNDimFreq()1500 int ModelMixture::getNDimFreq() {
1501 int dim = 0;
1502 int num_empirical = 0;
1503 int num_codon_1x4 = 0;
1504 int num_codon_3x4 = 0;
1505 for (iterator it = begin(); it != end(); it++) {
1506 // 2016-03-06: count empirical freq only once (thanks to Stephen Crotty)
1507 switch ((*it)->freq_type) {
1508 case FREQ_EMPIRICAL:
1509 num_empirical++;
1510 if (num_empirical==1)
1511 dim += (*it)->getNDimFreq();
1512 break;
1513 case FREQ_CODON_1x4:
1514 num_codon_1x4++;
1515 if (num_codon_1x4==1)
1516 dim += (*it)->getNDimFreq();
1517 break;
1518 case FREQ_CODON_3x4:
1519 case FREQ_CODON_3x4C:
1520 num_codon_3x4++;
1521 if (num_codon_3x4==1)
1522 dim += (*it)->getNDimFreq();
1523 break;
1524 default:
1525 dim += (*it)->getNDimFreq();
1526 }
1527 }
1528 return dim;
1529 }
1530
targetFunk(double x[])1531 double ModelMixture::targetFunk(double x[]) {
1532 getVariables(x);
1533 // decomposeRateMatrix();
1534 int dim = 0;
1535 for (iterator it = begin(); it != end(); it++) {
1536 if ((*it)->getNDim() > 0)
1537 (*it)->decomposeRateMatrix();
1538 dim += ((*it)->getNDim());
1539 }
1540 ASSERT(phylo_tree);
1541 if (dim > 0) // only clear all partial_lh if changing at least 1 rate matrix
1542 phylo_tree->clearAllPartialLH();
1543 // if (prop[size()-1] < 0.0) return 1.0e+12;
1544 return -phylo_tree->computeLikelihood();
1545 }
1546
optimizeWeights()1547 double ModelMixture::optimizeWeights() {
1548 // first compute _pattern_lh_cat
1549 phylo_tree->computePatternLhCat(WSL_MIXTURE);
1550 size_t ptn, c;
1551 size_t nptn = phylo_tree->aln->getNPattern();
1552 size_t nmix = getNMixtures();
1553
1554 double *new_prop = aligned_alloc<double>(nmix);
1555 double *ratio_prop = aligned_alloc<double>(nmix);
1556
1557 // EM algorithm loop described in Wang, Li, Susko, and Roger (2008)
1558
1559 for (int step = 0; step < optimize_steps; step++) {
1560 // E-step
1561
1562 if (step > 0) {
1563 // convert _pattern_lh_cat taking into account new weights
1564 for (ptn = 0; ptn < nptn; ptn++) {
1565 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix;
1566 for (c = 0; c < nmix; c++) {
1567 this_lk_cat[c] *= ratio_prop[c];
1568 }
1569 }
1570 }
1571 memset(new_prop, 0, nmix*sizeof(double));
1572 for (ptn = 0; ptn < nptn; ptn++) {
1573 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix;
1574 double lk_ptn = phylo_tree->ptn_invar[ptn];
1575 // double lk_ptn = 0.0;
1576 for (c = 0; c < nmix; c++) {
1577 lk_ptn += this_lk_cat[c];
1578 }
1579 ASSERT(lk_ptn != 0.0);
1580 lk_ptn = phylo_tree->ptn_freq[ptn] / lk_ptn;
1581 for (c = 0; c < nmix; c++) {
1582 new_prop[c] += this_lk_cat[c] * lk_ptn;
1583 }
1584 }
1585 bool converged = true;
1586 // double new_pinvar = 0.0;
1587 for (c = 0; c < nmix; c++) {
1588 new_prop[c] /= phylo_tree->getAlnNSite();
1589 // Make sure that probabilities do not get zero
1590 if (new_prop[c] < 1e-10) new_prop[c] = 1e-10;
1591 // check for convergence
1592 converged = converged && (fabs(prop[c]-new_prop[c]) < 1e-4);
1593 ratio_prop[c] = new_prop[c] / prop[c];
1594 if (std::isnan(ratio_prop[c])) {
1595 cerr << "BUG: " << new_prop[c] << " " << prop[c] << " " << ratio_prop[c] << endl;
1596 }
1597 prop[c] = new_prop[c];
1598 // new_pinvar += prop[c];
1599 }
1600 /*
1601 new_pinvar = 1.0 - new_pinvar;
1602 if (new_pinvar != 0.0) {
1603 converged = converged && (fabs(phylo_tree->getRate()->getPInvar()-new_pinvar) < 1e-4);
1604 phylo_tree->getRate()->setPInvar(new_pinvar);
1605 phylo_tree->getRate()->setOptimizePInvar(false);
1606 phylo_tree->computePtnInvar();
1607
1608 }
1609 */
1610 if (converged) break;
1611
1612 }
1613
1614 aligned_free(ratio_prop);
1615 aligned_free(new_prop);
1616 // aligned_free(lk_ptn);
1617 return phylo_tree->computeLikelihood();
1618 }
1619
optimizeWithEM(double gradient_epsilon)1620 double ModelMixture::optimizeWithEM(double gradient_epsilon) {
1621 size_t ptn, c;
1622 size_t nptn = phylo_tree->aln->getNPattern();
1623 size_t nmix = size();
1624
1625 double *new_prop = aligned_alloc<double>(nmix);
1626 PhyloTree *tree = new PhyloTree;
1627
1628 // attach memory to save space
1629 tree->central_partial_lh = phylo_tree->central_partial_lh;
1630 tree->central_scale_num = phylo_tree->central_scale_num;
1631 tree->central_partial_pars = phylo_tree->central_partial_pars;
1632
1633 tree->copyPhyloTree(phylo_tree);
1634 tree->optimize_by_newton = phylo_tree->optimize_by_newton;
1635 tree->setParams(phylo_tree->params);
1636 tree->setLikelihoodKernel(phylo_tree->sse);
1637 tree->setNumThreads(phylo_tree->num_threads);
1638
1639 // initialize model
1640 ModelFactory *model_fac = new ModelFactory();
1641 model_fac->joint_optimize = phylo_tree->params->optimize_model_rate_joint;
1642 // model_fac->unobserved_ptns = phylo_tree->getModelFactory()->unobserved_ptns;
1643
1644 RateHeterogeneity *site_rate = new RateHeterogeneity;
1645 tree->setRate(site_rate);
1646 site_rate->setTree(tree);
1647
1648 model_fac->site_rate = site_rate;
1649 tree->model_factory = model_fac;
1650 tree->setParams(phylo_tree->params);
1651 double prev_score = -DBL_MAX, score;
1652
1653 // int num_steps = 100000; //SC
1654 int step;
1655
1656 // EM algorithm loop described in Wang, Li, Susko, and Roger (2008)
1657 for (step = 0; step < optimize_steps; step++) {
1658 // first compute _pattern_lh_cat
1659 score = phylo_tree->computePatternLhCat(WSL_MIXTURE);
1660
1661 if (score < prev_score + gradient_epsilon)
1662 break;
1663 prev_score = score;
1664
1665 memset(new_prop, 0, nmix*sizeof(double));
1666
1667 // E-step
1668 // decoupled weights (prop) from _pattern_lh_cat to obtain L_ci and compute pattern likelihood L_i
1669 for (ptn = 0; ptn < nptn; ptn++) {
1670 double *this_lk_cat = phylo_tree->_pattern_lh_cat + ptn*nmix;
1671 double lk_ptn = phylo_tree->ptn_invar[ptn];
1672 // double lk_ptn = 0.0;
1673 for (c = 0; c < nmix; c++) {
1674 lk_ptn += this_lk_cat[c];
1675 }
1676 ASSERT(lk_ptn != 0.0);
1677 lk_ptn = phylo_tree->ptn_freq[ptn] / lk_ptn;
1678
1679 // transform _pattern_lh_cat into posterior probabilities of each category
1680 for (c = 0; c < nmix; c++) {
1681 this_lk_cat[c] *= lk_ptn;
1682 new_prop[c] += this_lk_cat[c];
1683 }
1684 }
1685
1686 // M-step, update weights according to (*)
1687
1688 bool converged = !fix_prop;
1689
1690 if (phylo_tree->isMixlen() && isFused() && !phylo_tree->getRate()->getFixParams()) {
1691 // update the weights for rate model
1692 converged = true;
1693 double new_pinvar = 0.0;
1694 for (c = 0; c < nmix; c++) {
1695 new_prop[c] = new_prop[c] / phylo_tree->getAlnNSite();
1696 if (new_prop[c] < 1e-10) new_prop[c] = 1e-10;
1697 // check for convergence
1698 converged = converged && (fabs(phylo_tree->getRate()->getProp(c) - new_prop[c]) < 1e-4);
1699 phylo_tree->getRate()->setProp(c, new_prop[c]);
1700 new_pinvar += new_prop[c];
1701 }
1702 new_pinvar = fabs(1.0 - new_pinvar);
1703 if (new_pinvar > 1e-6) {
1704 converged = converged && (fabs(phylo_tree->getRate()->getPInvar()-new_pinvar) < 1e-4);
1705 phylo_tree->getRate()->setPInvar(new_pinvar);
1706 // phylo_tree->getRate()->setOptimizePInvar(false);
1707 phylo_tree->computePtnInvar();
1708 }
1709
1710 } else if (!fix_prop) {
1711 // double new_pinvar = 0.0;
1712 for (c = 0; c < nmix; c++) {
1713 new_prop[c] = new_prop[c] / phylo_tree->getAlnNSite();
1714 if (new_prop[c] < 1e-10) new_prop[c] = 1e-10;
1715 // check for convergence
1716 converged = converged && (fabs(prop[c]-new_prop[c]) < 1e-4);
1717 prop[c] = new_prop[c];
1718 // new_pinvar += prop[c];
1719 }
1720 /*
1721 new_pinvar = 1.0 - new_pinvar;
1722 if (new_pinvar != 0.0) {
1723 converged = converged && (fabs(phylo_tree->getRate()->getPInvar()-new_pinvar) < 1e-4);
1724 phylo_tree->getRate()->setPInvar(new_pinvar);
1725 phylo_tree->getRate()->setOptimizePInvar(false);
1726 phylo_tree->computePtnInvar();
1727 }
1728 */
1729 }
1730
1731 // now optimize model one by one
1732 for (c = 0; c < nmix; c++) if (at(c)->getNDim() > 0) {
1733 tree->copyPhyloTreeMixlen(phylo_tree, c);
1734 ModelMarkov *subst_model;
1735 subst_model = at(c);
1736 tree->setModel(subst_model);
1737 subst_model->setTree(tree);
1738 model_fac->model = subst_model;
1739
1740 // initialize likelihood
1741 tree->initializeAllPartialLh();
1742 // copy posterior probability into ptn_freq
1743 tree->computePtnFreq();
1744 double *this_lk_cat = phylo_tree->_pattern_lh_cat+c;
1745 for (ptn = 0; ptn < nptn; ptn++)
1746 tree->ptn_freq[ptn] = this_lk_cat[ptn*nmix];
1747 subst_model->optimizeParameters(gradient_epsilon);
1748 // reset subst model
1749 tree->setModel(NULL);
1750 subst_model->setTree(phylo_tree);
1751
1752 }
1753
1754 phylo_tree->clearAllPartialLH();
1755 if (converged) break;
1756 }
1757
1758 // deattach memory
1759 tree->central_partial_lh = NULL;
1760 tree->central_scale_num = NULL;
1761 tree->central_partial_pars = NULL;
1762
1763 delete tree;
1764 aligned_free(new_prop);
1765 score = phylo_tree->computeLikelihood();
1766 phylo_tree->clearAllPartialLH();
1767 return score;
1768 }
1769
isFused()1770 bool ModelMixture::isFused() {
1771 for (int i = 0; i < size(); i++) {
1772 if (prop[i] != 1.0)
1773 return false;
1774 }
1775 return true;
1776 }
1777
optimizeParameters(double gradient_epsilon)1778 double ModelMixture::optimizeParameters(double gradient_epsilon) {
1779 optimizing_submodels = true;
1780
1781 int dim = getNDim();
1782 double score = 0.0;
1783
1784 if (!phylo_tree->getModelFactory()->unobserved_ptns.empty())
1785 outError("Mixture model +ASC is not supported yet. Contact author if needed.");
1786
1787 if (dim > 0)
1788 score = optimizeWithEM(gradient_epsilon);
1789 else if (!fix_prop)
1790 score = optimizeWeights();
1791
1792 // double score = ModelGTR::optimizeParameters(gradient_epsilon);
1793 optimizing_submodels = false;
1794 if (getNDim() == 0) return score;
1795 // now rescale Q matrices to have proper interpretation of branch lengths
1796
1797 double sum;
1798 int i, ncategory = size();
1799 for (i = 0, sum = 0.0; i < ncategory; i++) {
1800 sum += prop[i]*at(i)->total_num_subst;
1801 }
1802 // sum += phylo_tree->getRate()->getPInvar();
1803 if (fabs(sum-1.0) > 1e-6 && !isFused()) {
1804 for (i = 0; i < ncategory; i++)
1805 at(i)->total_num_subst /= sum;
1806 decomposeRateMatrix();
1807 phylo_tree->clearAllPartialLH();
1808 }
1809 return score;
1810 }
1811
isUnstableParameters()1812 bool ModelMixture::isUnstableParameters() {
1813 int c, ncategory = size();
1814 for (c = 0; c < ncategory; c++)
1815 if (prop[c] < MIN_MIXTURE_PROP*0.1) {
1816 outWarning("The mixture model might be overfitting because some mixture weights are estimated close to zero");
1817 break;
1818 return true;
1819 }
1820 return false;
1821 }
1822
decomposeRateMatrix()1823 void ModelMixture::decomposeRateMatrix() {
1824 for (iterator it = begin(); it != end(); it++)
1825 (*it)->decomposeRateMatrix();
1826 }
1827
setVariables(double * variables)1828 void ModelMixture::setVariables(double *variables) {
1829 int dim = 0;
1830 for (iterator it = begin(); it != end(); it++) {
1831 (*it)->setVariables(&variables[dim]);
1832 dim += (*it)->getNDim();
1833 }
1834 // if (fix_prop) return;
1835 // int i, ncategory = size();
1836
1837 // variables[dim+1] = prop[0]*at(0)->total_num_subst;
1838 // for (i = 2; i < ncategory; i++)
1839 // variables[dim+i] = variables[dim+i-1] + prop[i-1]*at(i-1)->total_num_subst;
1840
1841 // variables[dim+1] = prop[0];
1842 // for (i = 2; i < ncategory; i++)
1843 // variables[dim+i] = variables[dim+i-1] + prop[i-1];
1844
1845 // BQM 2015-05-19: modify using the same strategy for FreeRate model (thanks to Thomas Wong)
1846 // for (i = 0; i < ncategory-1; i++) {
1847 // variables[dim+i+1] = prop[i] / prop[ncategory-1];
1848 // if (variables[dim+i+1] < MIN_MIXTURE_PROP*0.9 || variables[dim+i+1] > MAX_MIXTURE_PROP) {
1849 // outWarning("For component " + convertIntToString(i+1) + ", mixture weight " + convertDoubleToString(variables[dim+i+1]) + " is out of bound and may cause numerical instability");
1850 // }
1851 // }
1852
1853 }
1854
getVariables(double * variables)1855 bool ModelMixture::getVariables(double *variables) {
1856 int dim = 0;
1857 bool changed = false;
1858 for (iterator it = begin(); it != end(); it++) {
1859 changed |= (*it)->getVariables(&variables[dim]);
1860 dim += (*it)->getNDim();
1861 }
1862 // if (fix_prop) return;
1863 // int i, ncategory = size();
1864
1865 // double *y = new double[ncategory+1];
1866 // y[0] = 0; y[ncategory] = 1.0;
1867 // memcpy(y+1, variables+dim+1, (ncategory-1) * sizeof(double));
1868 // std::sort(y+1, y+ncategory);
1869 // double sum = 0.0;
1870 // for (i = 0; i < ncategory; i++) {
1871 // prop[i] = (y[i+1]-y[i]);
1872 // }
1873
1874 // BQM 2015-05-19: modify using the same strategy for FreeRate model (thanks to Thomas Wong)
1875 // double sum = 1.0;
1876 // for (i = 0; i < ncategory-1; i++) {
1877 // sum += variables[dim+i+1];
1878 // }
1879 // for (i = 0; i < ncategory-1; i++) {
1880 // prop[i] = variables[dim+i+1] / sum;
1881 // }
1882 // prop[ncategory-1] = 1.0 / sum;
1883
1884
1885 // for (i = 0, sum = 0.0; i < ncategory; i++)
1886 // sum += prop[i]*at(i)->total_num_subst;
1887 // for (i = 0; i < ncategory; i++)
1888 // at(i)->total_num_subst /= sum;
1889
1890 // if (verbose_mode >= VB_MAX) {
1891 // for (i = 0; i < ncategory; i++)
1892 // cout << "Component " << i << " prop=" << prop[i] << endl;
1893 // }
1894 // delete [] y;
1895
1896 return changed;
1897 }
1898
setBounds(double * lower_bound,double * upper_bound,bool * bound_check)1899 void ModelMixture::setBounds(double *lower_bound, double *upper_bound, bool *bound_check) {
1900 int dim = 0;
1901 for (iterator it = begin(); it != end(); it++) {
1902 (*it)->setBounds(&lower_bound[dim], &upper_bound[dim], &bound_check[dim]);
1903 dim += (*it)->getNDim();
1904 }
1905 // if (fix_prop) return;
1906 // int i, ncategory = size();
1907 // for (i = 1; i < ncategory; i++) {
1908 // lower_bound[dim+i] = MIN_MIXTURE_PROP;
1909 // upper_bound[dim+i] = MAX_MIXTURE_PROP;
1910 // bound_check[dim+i] = false;
1911 // }
1912 }
1913
writeInfo(ostream & out)1914 void ModelMixture::writeInfo(ostream &out) {
1915 int i;
1916 for (i = 0; i < size(); i++) {
1917 at(i)->writeInfo(out);
1918 }
1919 // if (fix_prop) return;
1920 if (isFused()) return;
1921
1922 cout << "Mixture weights:";
1923 for (i = 0; i < size(); i++)
1924 cout << " " << prop[i];
1925 cout << endl;
1926 }
1927
writeParameters(ostream & out)1928 void ModelMixture::writeParameters(ostream &out) {
1929 for (iterator it = begin(); it != end(); it++) {
1930 (*it)->writeParameters(out);
1931 }
1932 }
1933
getName()1934 string ModelMixture::getName() {
1935 if (name != "") return name;
1936 string retname = "MIX";
1937 retname += OPEN_BRACKET;
1938 for (iterator it = begin(); it != end(); it++) {
1939 if (it != begin()) retname += ",";
1940 retname += (*it)->getName();
1941 }
1942 retname += CLOSE_BRACKET;
1943 return retname;
1944 }
1945
getNameParams()1946 string ModelMixture::getNameParams() {
1947 if (full_name != "")
1948 return full_name;
1949 string retname = "MIX";
1950 retname += OPEN_BRACKET;
1951 for (iterator it = begin(); it != end(); it++) {
1952 if (it != begin()) retname += ",";
1953 retname += (*it)->getNameParams();
1954 }
1955 retname += CLOSE_BRACKET;
1956 return retname;
1957 }
1958