1{ 2 "analysis":{ 3 "info":"This analysis applies the Muse Gaut 94 (MG94) model with the GTR nucleotide rate component \n to estimate the single dN/dS ratio for the alignment, and report its confidence intervals derived using profile likelihood.\n There is an option to select a subset of branches for estimation, in which case a separate omega is estimated for the selected branches.\n ", 4 "version":"0.1", 5 "citation":"A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome (1994). _Mol Biol Evol_ 11 (5): 715-724", 6 "authors":"Sergei L Kosakovsky Pond", 7 "contact":"spond@temple.edu", 8 "requirements":"in-frame codon alignment and a phylogenetic tree. Multiple partitions with a NEXUS file also supported" 9 }, 10 "fits":{ 11 "Nucleotide GTR":{ 12 "Log Likelihood":-3531.963655447697, 13 "estimated parameters":24, 14 "AIC-c":7112.142172130845, 15 "Equilibrium frequencies":[ 16 [0.3563279857397504], 17 [0.1837789661319073], 18 [0.2402852049910873], 19 [0.2196078431372549] 20 ], 21 "Rate Distributions":{ 22 "Substitution rate from nucleotide A to nucleotide C":0.5482529321972486, 23 "Substitution rate from nucleotide A to nucleotide G":1, 24 "Substitution rate from nucleotide A to nucleotide T":0.264805832733209, 25 "Substitution rate from nucleotide C to nucleotide G":0.4876106791881865, 26 "Substitution rate from nucleotide C to nucleotide T":1.019842357841139, 27 "Substitution rate from nucleotide G to nucleotide T":0.3027177206743494 28 }, 29 "display order":0 30 }, 31 "Global MG94xREV":{ 32 "Log Likelihood":-3466.725353220038, 33 "estimated parameters":31, 34 "AIC-c":6996.530140607651, 35 "Equilibrium frequencies":[ 36 [0.04785168648208005], 37 [0.03911346079312019], 38 [0.04842054060317301], 39 [0.04069665666515385], 40 [0.01817010744778396], 41 [0.01485205303123071], 42 [0.01838611113045968], 43 [0.01545321970309948], 44 [0.0190138898893362], 45 [0.01554175184587827], 46 [0.01923992433904378], 47 [0.01617083546230154], 48 [0.02796925133965702], 49 [0.02286176927319543], 50 [0.02830174586718859], 51 [0.02378714529482007], 52 [0.01687870337957799], 53 [0.01379647304851128], 54 [0.01707935503225849], 55 [0.01435491300079667], 56 [0.006409133648843443], 57 [0.005238757839512795], 58 [0.006485324528555602], 59 [0.005450807083377185], 60 [0.006706760641638982], 61 [0.005482034985409045], 62 [0.006786489669196017], 63 [0.005703931360295163], 64 [0.009865581170012171], 65 [0.008064021368173151], 66 [0.009982861811889655], 67 [0.008390428826966174], 68 [0.03287895020631181], 69 [0.02687490503171972], 70 [0.033269810543681], 71 [0.0279627207822247], 72 [0.01248470225271473], 73 [0.01020486315060615], 74 [0.01263311863778268], 75 [0.01061792547971484], 76 [0.01306446616325414], 77 [0.01067875601941112], 78 [0.01321977470017749], 79 [0.01111100011404158], 80 [0.01921770557551369], 81 [0.01570834862514353], 82 [0.01944616295744266], 83 [0.01634417558076203], 84 [0.01975257768318274], 85 [0.02055210293142003], 86 [0.009176034326710849], 87 [0.007500393094996483], 88 [0.00928511773266342], 89 [0.007803986567571961], 90 [0.00784869593340758], 91 [0.009716299514778986], 92 [0.008166387662818644], 93 [0.01412467213650941], 94 [0.01154535713247913], 95 [0.01429258425298098], 96 [0.01201267864744234] 97 ], 98 "Rate Distributions":{ 99 "0":[ 100 [0.996924216533022, 1] 101 ] 102 }, 103 "display order":1 104 }, 105 "omega":{ 106 "non-synonymous/synonymous rate ratio for *test*":{ 107 "LB":0.9083129274311988, 108 "MLE":0.996924216533022, 109 "UB":1.089831238806418 110 } 111 } 112 }, 113 "timers":{ 114 "Total time":{ 115 "timer":9, 116 "order":0 117 } 118 }, 119 "tested":{ 120 "0":{ 121 "PIG":"test", 122 "COW":"test", 123 "Node3":"test", 124 "HORSE":"test", 125 "CAT":"test", 126 "Node2":"test", 127 "RHMONKEY":"test", 128 "BABOON":"test", 129 "Node9":"test", 130 "HUMAN":"test", 131 "CHIMP":"test", 132 "Node12":"test", 133 "Node8":"test", 134 "Node1":"test", 135 "RAT":"test", 136 "MOUSE":"test" 137 } 138 }, 139 "input":{ 140 "file name":"/Users/sergei/Development/hyphy-develop/tests/hbltests/data/CD2.nex", 141 "number of sequences":10, 142 "number of sites":187, 143 "partition count":1, 144 "trees":{ 145 "0":"((((PIG:0.147969,COW:0.21343)Node3:0.085099,HORSE:0.165787,CAT:0.264806)Node2:0.058611,((RHMONKEY:0.002015,BABOON:0.003108)Node9:0.022733,(HUMAN:0.004349,CHIMP:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,RAT:0.050958,MOUSE:0.09795)" 146 } 147 }, 148 "data partitions":{ 149 "0":{ 150 "name":"single_omega.filter.default", 151 "coverage":[ 152 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186] 153 ] 154 } 155 }, 156 "branch attributes":{ 157 "0":{ 158 "HUMAN":{ 159 "original name":"HUMAN", 160 "Nucleotide GTR":0, 161 "Global MG94xREV":0 162 }, 163 "CHIMP":{ 164 "original name":"CHIMP", 165 "Nucleotide GTR":0.001819409505498532, 166 "Global MG94xREV":0.001830313020856732 167 }, 168 "BABOON":{ 169 "original name":"BABOON", 170 "Nucleotide GTR":0.001682207148475542, 171 "Global MG94xREV":0.001771862052542395 172 }, 173 "RHMONKEY":{ 174 "original name":"RHMONKEY", 175 "Nucleotide GTR":0.003775704995533204, 176 "Global MG94xREV":0.003718656169374045 177 }, 178 "COW":{ 179 "original name":"COW", 180 "Nucleotide GTR":0.248080655963153, 181 "Global MG94xREV":0.2481607489060679 182 }, 183 "PIG":{ 184 "original name":"PIG", 185 "Nucleotide GTR":0.1872739929226571, 186 "Global MG94xREV":0.1926123650858078 187 }, 188 "HORSE":{ 189 "original name":"HORSE", 190 "Nucleotide GTR":0.2089812616389708, 191 "Global MG94xREV":0.2112629012484836 192 }, 193 "CAT":{ 194 "original name":"CAT", 195 "Nucleotide GTR":0.2661351909060677, 196 "Global MG94xREV":0.2736352730879313 197 }, 198 "MOUSE":{ 199 "original name":"MOUSE", 200 "Nucleotide GTR":0.118210375708526, 201 "Global MG94xREV":0.1201852318281372 202 }, 203 "RAT":{ 204 "original name":"RAT", 205 "Nucleotide GTR":0.06676444909719663, 206 "Global MG94xREV":0.06704007343298489 207 }, 208 "Node1":{ 209 "Nucleotide GTR":0.2770985915795256, 210 "Global MG94xREV":0.2845062298344296 211 }, 212 "Node12":{ 213 "Nucleotide GTR":0.01784661013269995, 214 "Global MG94xREV":0.01788749017420944 215 }, 216 "Node2":{ 217 "Nucleotide GTR":0.06621080281260251, 218 "Global MG94xREV":0.06443131939831334 219 }, 220 "Node3":{ 221 "Nucleotide GTR":0.09881880264894725, 222 "Global MG94xREV":0.1016468208139953 223 }, 224 "Node8":{ 225 "Nucleotide GTR":0.1061558244712728, 226 "Global MG94xREV":0.1093725943478251 227 }, 228 "Node9":{ 229 "Nucleotide GTR":0.02566698049270639, 230 "Global MG94xREV":0.02593408269150705 231 } 232 }, 233 "attributes":{ 234 "original name":{ 235 "attribute type":"node label", 236 "display order":-1 237 }, 238 "Nucleotide GTR":{ 239 "attribute type":"branch length", 240 "display order":0 241 }, 242 "Global MG94xREV":{ 243 "attribute type":"branch length", 244 "display order":1 245 } 246 } 247 } 248}