1#NEXUS
2
3[
4Generated by HYPHY .99beta(MP) for MacOS(Carbon) on Fri Jul 30 16:05:23 2004
5
6]
7
8BEGIN TAXA;
9	DIMENSIONS NTAX = 25;
10	TAXLABELS
11		'RUFESCENS' 'SORENSENI' 'WALALLENSIS' 'KAMTSCHATKANA' 'SIEBOLDII' 'DISCUS_HANNAI' 'GIGANTEA' 'CORRUGATA' 'CRACHERODII' 'FULGENS' 'ROEI' 'SCALARIS' 'LAEVIGATA' 'CYCLOBATES' 'RUBRA' 'CONICOPORA' 'PUSTULATA' 'MIDAE' 'OVINA' 'DIVERSICOLOR' 'VARIA' 'AUSTRALIS' 'TUBERCULATA' 'COCCINEA' 'IRIS' ;
12END;
13
14BEGIN CHARACTERS;
15	DIMENSIONS NCHAR = 402;
16	FORMAT
17		DATATYPE = DNA
18
19		GAP=-
20		MISSING=?
21	;
22
23MATRIX
24	'RUFESCENS'      CGCAGCTGGCATTATGTTGAACCCAAGTTTTTAAACAAGGCTTTTGAAGTTGCACTGAAGGTACAGATCATTGCTGGATTCGATAGAGGGCTGGTCAAATGGCTTAGAGTTCATGGCAGAACATTGTCTACCGTTCAGAAGAAGGCGCTGTACTTCGTCAATAGACGTTACATGCAGACCCACTGGGCGAATTACATGCTCTGGATAAATAAGAAGATCGATGCACTGGGCAGAACTCCAGTTGTTGGTGACTACACACGGTTAGGTGCCGAAATTGGAAGACGTATTGATATGGCTTACTTTTACGACTTCCTGAAAGATAAGAACATGATCCCAAAATATCTGCCATACATGGAAGAAATTAATAGAATGCGCCCGGCAGATGTCCCAGTTAAATACATG
25	'SORENSENI'      CGCCGCTGGCATTATGTTCCACCCAAGTTTTTAAACAAGGCTTTTGAAGTTGCACTGAAGGTACAGATCATTGCTGGATTCGATAGAACGCTGGTCAAATGGCTTAGAACTCATGGCGGAACATTGTCTCACGTTCAGAAGAAGGCGCTGTACTTCGTCAATAGACGTTACATGCAGACCCACTGGGCGAACTACATGCTCTGGATAAATAAGAAGACCGATGCACTGGGCAGAACTCCAGTTGTTGGTGACTACACACGGTTAGGTGCCGAAATTGGAAGACGTATTGATATGGATTACTTTTACAACTTCCTGAAAGGGAGGAACATGATCCCAAAATATCTGCCATACATGGAAGAAATTAATAGAATGCGCTCGGCAGATATCCCAGTTAAATACATG
26	'WALALLENSIS'    CGCCGCTGGAATTTTGTTACACCCAGGGAGGTAAACAAGGCTTTTGAAGTTGCACTGAAGGTACAGATCATTGCTGGATTCGATAGAACGCTGGTCAAATGGCTTAGAGCTCATGGCAGATCATTGTCTCACGTTCAGAAGAAGGCGCTGTACTTCGTCAATAGACGTTACATGCAGACCCACTGGGCGAATTACATGCTCTGGGTAAATAAGAAGATCGATGCACTGGGCAGAACTGCAGTTGTTGCTGACTACACACGGTTAGGTGCCGAAATTGGAAGACGTATTGACATGGATTACTTTTACAACTTCCTGAAAGGAAGGAACATGATCCCAAAATATCTGCCATACATGGAAGAAATTAATAGAATGCGCTCGGCAGATATCCCAATTAGATAC---
27	'KAMTSCHATKANA'  CGCAGCTGGACTTATGTTCAACCCAAGTTTTTAAACAAGGCTTTTGAAGTTGCACTGAAGGAAGAGATCATTGTTCGATGGGATAGAAAGCTGGCCAAATGGCTTAGAGTTAATGGCGGACCATTGTCTCACGTTCAGAAGAAGGCGCTGTACTTCGTCAATAGACGTTACATGCAGACCCACTGGGCGAATTACATGCTCTGGATAAATAAGAAGACCGATGCACTGGGCAGAACTCCAGTTGTTGGTGACTACAGACGGTTAGGTGCCGAAATTGGAAGACGTATTGATATGGTTTTCTTTTACAAATTCCTGTCAGGGAGGAACATGATCCCAAAATATATGCCATACATGGAGCAGATTAATAGAATGCGCGCGGCAGATATCCCAGTTAAATACATG
28	'SIEBOLDII'      CGCCGCTGGCATTTTGTTCAACATCAGTATGTAGACAAGGCTTTTGAAATTGCACTGAAGGAAGAGATCGTTGCTGGATTCGACAGAACGCTGGTCAAATGGCTTAGAGTTCATGGCAGAGGTTTGACTCCAGTTCAGAAGAAGGCGCTGTACTTCGTCAATAGACGTTACATGCAGACCCACTGGCAGAATTACATGCTCTGGATAGTCAAGAAGATCGATGCACTGGGCAGAACTCCAGTTGTTGGTGACTACAGACGGTTAGGTGCCGAAATTGGAAGACGTATTGATATGGATTATTTTTACAACTTCCTGAAAAATAGGAACATGATCCCAAAATATATGCCATACATGGAAGAACTTAATAGAATGCCCGCGAGAGATATCCCAGTTAAAAAC---
29	'DISCUS_HANNAI'  CGCCGCTGGAATTTTGTTCGACATCAGTATGTAAACAAGGCTTTTGAAATTGCACTGAAGGAAGAGATCGTTGCTGGATTCGATAGAACGCTGAACAAATGGCTTAGCGCTCATGGCAGAGGTTTGACTCCAGATCAGAGGAAGGCGCTGTTCTTCGTCAATAGACGTTACATGCAGACCCACTGGCAGAATTACATGCTCTGGGTAGTGAAGAAGATCGATGCACTGGGCAGAACTCCAGTTGTTGCTGACTACAGACGGTTAGGTGCCGAAATTGGAAGACGTATTGATATGGATTATTTTTACAACTTCCTGAAAAATAGGAACATGATCCCAAAATATGTGAGATACATGGCCGCACTTAATAGAATGCCAGCGAGAGATATCCCAGTTAAAAAC---
30	'GIGANTEA'       CGCCGCTGGAATTTTGTTCGACATCAGTATGTAAACAAGGCTTTTGAAATTGCACTGAAGGAAGAGATCGTTGCTGGATTCGATAGAACGCTGAACAAATGGCTTAGCGCTCATGGCAGAGGTTTGACTCCAGATCAGAGGAAGGCGCTGTTCTTCGTCAATAGACGTTACATGCAGACCCACTGGCAGAATTACATGCTCTGGGTAGTGAAGAAGATCGATGCACTGGGCAGAACTCCAGTTGTTGCTGACTACAGACGGTTAGGTGCCGAAATTGGAAGACGTATTGATATGGATTATTTTTACAACTTCCTGAAAAATAGGAACATGATCCCAAAATATGTGGGATACATGGCCGAACTTAATAGAATGCCAGCGAGAGATATCCCAGTTAAAAAC---
31	'CORRUGATA'      CGCCGCTTCCGTTTTATTCCACATAAGTATATACGCAAGGAGTTTGAAGTTGCACTGAAGGTAGAGATCATTGCCGGATTCGATAGAACGCTGGTCAAATGGCTTAGAGTTCATGGCGGACGTTTGAGTACAGTTCAGAAGAAGGCGCTGTACTTCGTCAATAGACGTTACATGCAGACCCACTGGCAGAATTACATGCTCTGGATAGTGAGGAAGACCGATGCACTGGGCAGACCTCCAGTTGTTGCTGACTACAGTCGGTTAGGTGCCGAAATTGGAAGACGTATTGATATGGCATATTTTTACAACTTCCTGAACGGGAGGAACATGATCCCAAAATATCTGCCATACATGGAGGAAATTAATAGAATGCGCCCGGCAGATGTCCCAGTTGCAAAC---
32	'CRACHERODII'    CGCCGCTATCAATTTGTTCAACATCAGTATATTCGCAAGGCTTTTGAAGTTGCACTGAAGGTAGAGATCATTGCTGGATTCGACAGAACGCTGGTCAAATGGCTTAGAAATCATGGCAGAGGTTTGAATGAAAATCAGAGGAAGGTGCTGTACTTCGTCAATAGACGTTACATGCAGACCCACTGGCAGAATTACATGCTCTGGATAGTGAAGAAGACCAATGCACTGGGCAGACCTCCAGTTGTTGCTGACTACCGTGCGTTGGGTGCCGAAATTGGAAGACGTATTGATATGGGATATTTTTACAACTTCCTGAAAAATAGGGTCATGATCCCAAAATATTTGCCATACATGCGAAGACTTAATAATATGCGCCCGGAAGATGTCCCAGTTGCAAACAAC
33	'FULGENS'        CGCCGATGGACTTTTGTTCGATATCATTATATAAACAAGGCTTATGAAGTTACAATGAAGATACAGATCATTTCTGGATTCGATAGACAGCTGACCGCATGGCTCAGAGTTCATGGCAGACGTTTGACTAATAATCAGAAGAAGACGCTGTTCTTCGTCAATAGACGTTACATGCAGACCCACTGGCAGAATTACATGCTCTGGGTTAAGAGGAAGATCAAGGCACTGGGCAGACCCGCAGCTGTTGGTGACTACACTCGGTTAGGTGCCGAAATAGGAAGACGTGTTGATATGGTATTTTTTTACAACTTCCTGTCCGGGAGAAAAATGATCCCACCATACAGCGCATATATGGCAAAACTTAATGCCTTGCGCCCGGCAGATGTCCCAGTTAAAAAC---
34	'ROEI'           CGCCATTGGCACTTTGTTGCCCACAAACATGTTTCCAGGCCTTTTGAAGTTGCACTGAAGGTCCAGATCATTGCTGGGTTTGATAGACAGTTGGCCTCCTGGCTTCAACGTCATGGCAGGCGTTTAAGCGCAATTCAGAAGAAGACGCTGTACTTCGTTAATAGGCGTTACATGCAGACTCACTGGCAAGCTTACATGGTGTGGATAGTCAAGCAGATAGAAAAACTTGGTAGGTCACCCAACGTTGGCGACTACAGCTACGTTGGTGCCGAGATCGGAAGACGTATTCCTTTGGAAGTAACCTACAGCTTTTTGGTCAGGAGAAACTTGATCCCTCAATGGCGTCAGTACATGGCAAACCTTATGGCCAAACGCGTGGAAGATATCCCAGTT---------
35	'SCALARIS'       CGCCGATGGGTCTTTACGCCCCACAAACATGTTGCCAGGCAATTTGAAGTTGCACTGAAGGTCCAGATCATTGCTGGGTTTGATAGAAAGTTGGTTAACTGGCTTCGACGTCATGGCAAGTATGTGAGCGCAATTCAGAGGAAGTCGCTGTACTTCGTTAATAGGCGTTACATGCAGACTCACTGGCAAGCTTACATGGTGTGGATAGTCAAGCAAGTAGCCAAACTTGGTAGGCCACCCACCGTTAGCGACTACAGCTACGTTGGTGCCGAGATCGGAAGACGTATTCCTTTGGAAGTAACCTACAGCTTTTTGGTCAGGAGAAACTTGATCCCTGAAATGCGTCAGTACATGAGAGACCTTAATGCCAAACGCGTGGAAGATATCCCAGTT---------
36	'LAEVIGATA'      CGCCGATGGCACTTTGTTCCCCACACACATGTTGCCAGGCCTTTTGAAGTTGCACTGAAGGTCCAGATCATTGCTGGGTTTGATAGAAAGTTGGTTGCCTGGCTTCAACGTCATGGCAGGCATCTAAGCGCAATTCAGAAGAAGTCGCTGTACTTCGTTAATAGGCGTTACATGCAGACTCACTGGCAAGCTTACATGGTGTGGATAGCTAAGCAAGTAGCCAAACTTGGTAGGGCACCCACCGTTAACGACTACAGTCGCATTGGTGCCGAGATCGGAAGACGTATTCCTTTGGAAGTAACCTACAGCTTTTTGGTCAGGAGAAACTTGATCCCTCGAATGCGTCAGTTCATGAGAGACCTTATTGCCAAACCCGTGCAAGATATCCCAATT---------
37	'CYCLOBATES'     CGCCGATGGCACTTTACTGCCCACAGGAGAATTTCCAGGCGTTTTGAAGCTGCACTGAAGGTCCAGATCATTCTTGGGTTTGATAAAAAGTTGGCCACCTGGCTTGCACGTTATGGCAAGAATTTGAGCGCAATTCATAAGAAGACGCTGTACTTCTATAATAGGCGTCACATGCAGACTCACTGGCAATCCTACATGAGGTTCACAGAGAAGGATATAAGAAAACTTGGTAGGCCACCCAACAGTAACGACTACACTCGCATTGGTGCCGAGATCGGAAGACGTATTCCTATTGAATTGATGTACAGCTTTATGGTCAGGAGAAACATGATCCCTAGATGGCGTCCGTATATGGGAGTCCTTCTGTCCAAACGCAAGGAAGATATCCCAGTTAAT------
38	'RUBRA'          CGCCGATGGCACTTTGTTGCCCACAGACATGTTTCCAGGCAATTTGAAGTTGCACTGAAGGTCCAGATCATGGCTGGGTTTGATAAAAAGTTGACCAATTGGCTTGCACGTCATGGCAGGAATTTGAGCCCAATTCAGAAGAAGACGCTGTACTTCGTTAATAGGCGTTACATGCAGACTCACTGGCAGATGTACATGCAGTTCATAGTCAAGGAGATAGACAAACTTGGTAGGGCACCCAACGTTAACGACTACAGTCGCGTTGGTGCCGAGATCGGAAGACGTATTCCTCTGGAAGTAACCTACAGCTTTTTGGTCAGGAGAAACTTGATCCCTAGATGGCGTCAGTACATGGGAAACCTTCTGGCCAAACGCGTGGAAAATATCCCAATT---------
39	'CONICOPORA'     CGCCGATGGCACTTTGTTGCCCACAGACATGTTTCCAGGCAATTTGAAGTTGCACTGAAGGTCCAGATCATGGCTGGGTTTGATAAAAAGTTGGCCAATTGGCTTGCACGTCATGGCAGGAATTTGAGCCCAATTCAGAAGAAGACGCTGTACTTCGTTAATAGGCGTTACATGCAGACTCACTGGCAGATGTACATGCAGTTCATAGTCAAGGAGATAAACAAACTTGGTAGGGCACCCAACGTTAACGACTACAGTCGCGTTGGTGCCGAGATCGGAAGACGTATTCCTCTGGAAGTAACCTACAGCTTTTTGGTCAGGAGAAACTTGATCCCTAGATGGCGTCAGTACATGGGAAACCTTCTGGCCAAACGCGTGGAAAATATCCCAATT---------
40	'PUSTULATA'      CGCCACTGGGGCTTTGTTCCACACAGACGTCTTGCCAGGCAATTTGAAGTTGCACTGAAGGTACAGATCATCGCTGGGTTTGATAGAAAATTGTCTGGCTGGCTTACCCGTCATGGCAGTCGTTTAAGTCCAATTCAGAGGAAGACGCTGTACTTTGTCAACAGACGTTATATGCAGACTCTCTGGCAAAACTACTTTCGGTTCGTAGCGAGGAGAATCGGCAAACTTGGAAGGGCTCCCAACGTGAACGACTACAATGCCGTAGGTGCCGAAATCGGAAGACGTGTTCCTTTGGAAGTGACCTATAGCTTTTTGGTCAGGCGAAACTTGATCCCAACTTGGCGTCAGTACATGGCAAATCTTTTGGCCAGACGTGTGGAAGATATCCCAGTT---------
41	'MIDAE'          CGCCGTTTTTATTTTATTAGGCACCAGTATCTTGCCAAGCCATTTGAAGTTGCACTCAAGGTACAGATCGTTGCTGGGTTTGACAGAAAGTTGACTGCCTGGCTTCGACGTCATGGCAGCCATGTGAGCGCAATTAAGAGGAAGACGCTGTACTTCGTTAATAGACGTTACATGCAGACTCACTGGCAAGCCTACATGGTGTGGATTGTCAGGAAGATCAAAGCACTTGGAAGGCCACCCACCGTCGCAGATTACACTGCACTTGGTGCCGAGATCGGAAGACGTATTCCTTTGGAAGTAACCTACAGCTTTTTGGTCAGGAGAAACTTGATCCCTTCCTGGCGTCCGTACATGGCAAGACTTATGGCCAAACGTCCGGCAGATATCCCAATT---------
42	'OVINA'          CGCCGTTGGGCCTTTATTCCCCCCACACGTATTCCCAGGGCTCATGAAGTTGCACTGAAGGTACAGATCATTGCTGGCTGGAACAGAAAGCTGGCCAACTGGCTTGCACGACATGGCAGTCGTTTGAGTGCAATTCAGAAGAAGACGCTGTACTTTGTGAACAGACGTTATATGCAGACTCACTGGCCATCCTACATGATATTTGTCAAGAAGCAGATAGCTAGACTTGGTAGGCCAGGCAACACTAACGACTACAGTCGCCTGGGTGCCGAGATCGGAAGACGTATTCCTATGGAAGTAAACTACAGCTTTCTGGTCAGGAGAAACTTGATCCCACGATGGCGTCAGTACATGGCAAACCTCATGGCCAAACGCGTGGAAGATATCCCAGTT---------
43	'DIVERSICOLOR'   CGCGGTTGGGGCTATATTCCCCGCACACGTCTAAACAGGGCTTTTGAAGTTGCACTGAAGGTGCAGATCATCGCTGGGTTTGATAGAAAGCTGACCAGCTGGCTTGGACGCCATGGTAGTCGTTTGAGTGCAATTCAGAGGAAGACGCTGTACTTCGTTAACAGGCGCTATCTGCAAACTCACTGGTCAGCCTACATGGTTTGGATAAACAAGCGGATAGCCGCACTTGGTAGAACAGCCACGACTGCAGACTACAATAACCTTGGTGCCGAGATCGGAAGACGTATTCCTATGGAAGTAACATACAGCTTTTTGGTCAGGAGAAACTTGATCCCCAAATGGCGTCCATATATGGCAGCCATTATGGCCAAATCAGCGGCAGATCTTGAAGTTGCA------
44	'VARIA'          CGCCGTTGGACCTTTATTCCGCGCAAACGTCTTCCGATGGCTCATGAAGTTGCATTAAAGGTAGAGATCATTGCTGGGTTCAACAAAAAACTGGACATCTGGCTTGCACGACATGGCAGTCGTTTGAGTCCAATTCAGAAGAAGACGCTGTACTTTGTGAACAGACGTTATATGCAGACTCACTGGTCTAATTACATGTTGTGGGTTAAAAGGCGGATAAATAGTCTTGGAAGGCCAGGTACTACGGCAGACTACAGAAACCTCGGTGCTGAGATTGGAAGACGTGTTCCTTTGGAATTAACCTATAGCTTTTTGGTCCGGAGAAACTTGATCCCACAATGGCGTCAGTACATGGCAGACCTTATGGCCAGACGCGTGGCAGATATCCCAGTTGCA------
45	'AUSTRALIS'      CGCCGTTGGAGATTTGTTCCCCACGTACAAGTTAACAGGTCTTTTGAAGTGGCACTGAAGGTACAGATCATTGCTGGGTTTGATAGAAAGTTGACAAGCTGGCTTTCACGTCATGGGCGTCGTCTGAACGCAGTTCAGAGGAAGACGTTGTACTTCGTCAACAGACGTTACATGCAGACTCACTGGCAATCTTACATGGTGTGGATAAACAAGCAGATCGCCAAACTTGGAAGGACTGCCACCGATGCCGACTACGCTAGCGTTGGTGCCGAAATCGGAAGACGTATTCCTCTGGAACTTACCTACAGCTTTTTGGTCAGGAGAAACTTGATCCCAAGATGGCGCCCATACATGGCAGCCCTTATGGCCAAGCGCGTGCAAGATATCCCAGTTGCAAAT---
46	'TUBERCULATA'    ---------------------------CACCTTACCAGGCAATTTGAAGTTGCTCTGAAGGTACAGATCATTGCTGGGTTTGATAAAAAGTTGGCTACCTGGATTAACCGTCATGGCAGTGGTTTAAGCGCAGTTCAGAAGAAGACGCTGTACTTTGTCAACAGACGTTATATGCAGACTTACTGGCAAAACTACATGCTGTTCGTAGATGAGAAGATACGAAAACTTGGAAGGGCTCCCAACGTTAACGACTACACTGCCATCGGTGCCGAAATTGGAAGACGTGTTCCTTTGCAAATAACATACCCCATTATGATCAAGTACCACATTCTTCCAAAATGGCGTCCGTACATGGGAAAAATTTTGGCCCTACGTGTGGAAGATATCCCAGTTGATTAT---
47	'COCCINEA'       ---------------------------CAACTTACCAGGCAATTTGAAGTTGCTCTGAAGGTACAGATCATTGCTGGGTTTGATAAAAAGTTGGCTGCCTGGATTAACCGTCATGGCAGGGGTTTAAGTGCAGTTCAGAAGAAGACGCTGTACTTTGTCAACAGACGTTATATGCAGACTTACTGGCAAAACTACATGCTGTTCGTAGATGAGAAGATACGAAAACTTGGAAGGGCTCCCAACGTTAACGACTACACTGCCATCGGTGCCGAAATTGGAAGACGTGTTCCTTTGCAAATAACATACCCCATTTTGATCAAGTACAACATTCTTCCAAAATGGCATCCGTACATGGGGAAAGTTTTGAGCCTACGTGTGGAAGATATCCCAGTTGATTAT---
48	'IRIS'           ---GGGTGGGGCTATCCACCAGGGACCTTTTTATCAAAAGCTAAGTTAAGTGCACTGAAGACACAGATCATTGCTGGGTTCGATAGAAAGCTGGCCAGTTGGCTTAGACGTCATGGCAATCGTTTGAGCGCAATTCAGAAGAAGACGCTGTACTTCGTCAATAGACGTTACATGCAGACTCACTGGCGCTCTTACATGAAATTCGTACGAAATCAGATGAAATTACTTGGTAGAGCTGAAACCACTGCGGACTACAATCGCGTAGGTGCCGCAATTGGAAAACGCATTCCCTTGGAAATAACGTACAGCTTTTTAGTCAGGAGGAACTTGATACCTAAATGGAAACCGTACATGGCACGACTTATGGCCAGACGCCCAGGTGATATCCCAACTTCG------;
49END;
50
51BEGIN TREES;
52	TREE tree = ((FULGENS,(((KAMTSCHATKANA,(RUFESCENS,(SORENSENI,WALALLENSIS)NODE9)NODE7)NODE5,(SIEBOLDII,(DISCUS_HANNAI,GIGANTEA)NODE14)NODE12)NODE4,(CORRUGATA,CRACHERODII)NODE17)NODE3)NODE1,IRIS,((PUSTULATA,(COCCINEA,TUBERCULATA)NODE24)NODE22,(AUSTRALIS,((MIDAE,((ROEI,(SCALARIS,LAEVIGATA)NODE35)NODE33,(CYCLOBATES,(RUBRA,CONICOPORA)NODE40)NODE38)NODE32)NODE30,((OVINA,VARIA)NODE44,DIVERSICOLOR)NODE43)NODE29)NODE27)NODE21);
53END;
54
55BEGIN HYPHY;
56
57DATA_PANEL_SOURCE_PATH="";
58DataSet ys2002 = ReadDataFile (USE_NEXUS_FILE_DATA);
59DataSetFilter buried = CreateFilter (ys2002,3,"30-32,42-47,51-59,66-71,75-80,90-92,99-104,114-116,123-125,144-149,153-164,171-176,183-185,192-197,204-206,216-218,249-254,261-266,273-278,291-293,303-305,312-314,330-335,339-341,351-353,360-365,384-386,390-392,396-398","","TAA,TAG,TGA");
60DataSetFilter exposed = CreateFilter (ys2002,3,"0-29,33-41,48-50,60-65,72-74,81-89,93-98,105-113,117-122,126-143,150-152,165-170,177-182,186-191,198-203,207-215,219-248,255-260,267-272,279-290,294-302,306-311,315-329,336-338,342-350,354-359,366-383,387-389,393-395,399-401","","TAA,TAG,TGA");
61DataSetFilter GA1 = CreateFilter (ys2002,3,"0-2,6-8,12-14,21-23,36-38,42-92,99-104,108-116,123-128,132-185,192-197,201-203,210-212,216-218,225-242,249-254,264-296,300-317,321-335,339-341,348-353,360-371,381-392,396-398","","TAA,TAG,TGA");
62DataSetFilter GA2 = CreateFilter (ys2002,3,"3-5,9-11,15-20,24-35,39-41,93-98,105-107,117-122,129-131,186-191,198-200,204-209,213-215,219-224,243-248,255-263,297-299,318-320,336-338,342-347,354-359,372-380,393-395,399-401","","TAA,TAG,TGA");
63Tree Tree_1=((fulgens,(((kamtschatkana,(rufescens,(sorenseni,walallensis)Node9)Node7)Node5,(sieboldii,(discus_hannai,gigantea)Node14)Node12)Node4,(corrugata,cracherodii)Node17)Node3)Node1,iris,((pustulata,(coccinea,tuberculata)Node24)Node22,(australis,((midae,((roei,(scalaris,laevigata)Node35)Node33,(cyclobates,(rubra,conicopora)Node40)Node38)Node32)Node30,((ovina,varia)Node44,diversicolor)Node43)Node29)Node27)Node21);
64Tree Tree_13=((fulgens,(((kamtschatkana,(rufescens,(sorenseni,walallensis)Node9)Node7)Node5,(sieboldii,(discus_hannai,gigantea)Node14)Node12)Node4,(corrugata,cracherodii)Node17)Node3)Node1,iris,((pustulata,(coccinea,tuberculata)Node24)Node22,(australis,((midae,((roei,(scalaris,laevigata)Node35)Node33,(cyclobates,(rubra,conicopora)Node40)Node38)Node32)Node30,((ovina,varia)Node44,diversicolor)Node43)Node29)Node27)Node21);
65OpenDataPanel(ys2002,"","0,0,0,241,2,0,10","GY94_3x4,1,0,14443523,No_tree;GY94_3x4,1,0,212,No_tree;GY94_3x4,65537,0,25618,Tree_1;GY94_3x4,65537,0,5712645,Tree_13",ys2002_LF);
66
67global TS1=0.5485688128621145;
68global GA2_Shared_TVTS=0.6448047320534194;
69global GA2_Shared_DNDS=1.691911824567705;
70global GA1_Shared_DNDS=0.5996885198698069;
71global GA1_Shared_TVTS=0.5735572687833753;
72Tree_13.rubra.synRate=0.1412267165216146;
73Tree_13.sorenseni.synRate=0.2812521364812907;
74Tree_13.conicopora.synRate=0.03846144891039521;
75Tree_13.discus_hannai.synRate=0.1746410067358681;
76Tree_13.Node3.synRate=2.388499650721909;
77Tree_13.Node35.synRate=1.620983326221706;
78Tree_13.laevigata.synRate=1.301161626625689;
79Tree_13.Node33.synRate=0.01418341357917285;
80Tree_13.cyclobates.synRate=5.176566003017607;
81Tree_13.Node40.synRate=1.285491195569625;
82Tree_13.Node17.synRate=0.6103920652279604;
83Tree_13.Node38.synRate=1.916764582432429;
84Tree_13.Node32.synRate=0.847741832301011;
85Tree_13.Node30.synRate=1.353548466958184;
86Tree_13.scalaris.synRate=1.793466985777919;
87Tree_13.corrugata.synRate=1.508137924968129;
88Tree_13.Node22.synRate=3.586688183941883;
89Tree_13.Node24.synRate=4.811499981077868;
90Tree_13.iris.synRate=9.538992307798807;
91Tree_13.sieboldii.synRate=0.2525167033389518;
92Tree_13.fulgens.synRate=4.372003969431494;
93Tree_13.roei.synRate=1.292504197767953;
94Tree_13.midae.synRate=6.049508218703066;
95Tree_13.australis.synRate=3.807411363098394;
96Tree_13.rufescens.synRate=1.193899457926468;
97Tree_13.coccinea.synRate=0.7061986139311774;
98Tree_13.Node12.synRate=1.199370279201513;
99Tree_13.Node1.synRate=8.394124082856141;
100Tree_13.walallensis.synRate=1.585275626202918;
101Tree_13.Node7.synRate=0.2433775009386973;
102Tree_13.Node4.synRate=0.7484895466835784;
103Tree_13.Node5.synRate=1.971767674128962;
104Tree_13.kamtschatkana.synRate=2.11244551426108;
105Tree_13.tuberculata.synRate=0.3755503661102469;
106Tree_13.gigantea.synRate=0;
107Tree_13.cracherodii.synRate=3.419385143820095;
108Tree_13.Node21.synRate=2.012513393683696;
109Tree_13.Node44.synRate=1.826534376055297;
110Tree_13.diversicolor.synRate=5.129518926703711;
111Tree_13.Node9.synRate=0.2485807513302384;
112Tree_13.ovina.synRate=2.265661140231043;
113Tree_13.varia.synRate=4.607110378333808;
114Tree_13.pustulata.synRate=2.778444006733563;
115Tree_13.Node27.synRate=0.3508251312802478;
116Tree_13.Node14.synRate=1.594460725928353;
117Tree_13.Node29.synRate=0.5503958792831721;
118Tree_13.Node43.synRate=1.446206947755718;
119Tree_1.Node29.synRate:=TS1*Tree_13.Node29.synRate;
120Tree_1.Node7.synRate:=TS1*Tree_13.Node7.synRate;
121Tree_1.Node43.synRate:=TS1*Tree_13.Node43.synRate;
122Tree_1.Node12.synRate:=TS1*Tree_13.Node12.synRate;
123Tree_1.Node4.synRate:=TS1*Tree_13.Node4.synRate;
124Tree_1.diversicolor.synRate:=TS1*Tree_13.diversicolor.synRate;
125Tree_1.Node44.synRate:=TS1*Tree_13.Node44.synRate;
126Tree_1.kamtschatkana.synRate:=TS1*Tree_13.kamtschatkana.synRate;
127Tree_1.varia.synRate:=TS1*Tree_13.varia.synRate;
128Tree_1.ovina.synRate:=TS1*Tree_13.ovina.synRate;
129Tree_1.Node5.synRate:=TS1*Tree_13.Node5.synRate;
130Tree_1.tuberculata.synRate:=TS1*Tree_13.tuberculata.synRate;
131Tree_1.Node30.synRate:=TS1*Tree_13.Node30.synRate;
132Tree_1.Node32.synRate:=TS1*Tree_13.Node32.synRate;
133Tree_1.cracherodii.synRate:=TS1*Tree_13.cracherodii.synRate;
134Tree_1.gigantea.synRate:=TS1*Tree_13.gigantea.synRate;
135Tree_1.coccinea.synRate:=TS1*Tree_13.coccinea.synRate;
136Tree_1.Node1.synRate:=TS1*Tree_13.Node1.synRate;
137Tree_1.Node38.synRate:=TS1*Tree_13.Node38.synRate;
138Tree_1.Node40.synRate:=TS1*Tree_13.Node40.synRate;
139Tree_1.walallensis.synRate:=TS1*Tree_13.walallensis.synRate;
140Tree_1.Node14.synRate:=TS1*Tree_13.Node14.synRate;
141Tree_1.conicopora.synRate:=TS1*Tree_13.conicopora.synRate;
142Tree_1.rubra.synRate:=TS1*Tree_13.rubra.synRate;
143Tree_1.pustulata.synRate:=TS1*Tree_13.pustulata.synRate;
144Tree_1.cyclobates.synRate:=TS1*Tree_13.cyclobates.synRate;
145Tree_1.Node9.synRate:=TS1*Tree_13.Node9.synRate;
146Tree_1.Node33.synRate:=TS1*Tree_13.Node33.synRate;
147Tree_1.rufescens.synRate:=TS1*Tree_13.rufescens.synRate;
148Tree_1.Node35.synRate:=TS1*Tree_13.Node35.synRate;
149Tree_1.Node17.synRate:=TS1*Tree_13.Node17.synRate;
150Tree_1.laevigata.synRate:=TS1*Tree_13.laevigata.synRate;
151Tree_1.discus_hannai.synRate:=TS1*Tree_13.discus_hannai.synRate;
152Tree_1.sorenseni.synRate:=TS1*Tree_13.sorenseni.synRate;
153Tree_1.scalaris.synRate:=TS1*Tree_13.scalaris.synRate;
154Tree_1.roei.synRate:=TS1*Tree_13.roei.synRate;
155Tree_1.Node3.synRate:=TS1*Tree_13.Node3.synRate;
156Tree_1.midae.synRate:=TS1*Tree_13.midae.synRate;
157Tree_1.australis.synRate:=TS1*Tree_13.australis.synRate;
158Tree_1.fulgens.synRate:=TS1*Tree_13.fulgens.synRate;
159Tree_1.Node22.synRate:=TS1*Tree_13.Node22.synRate;
160Tree_1.sieboldii.synRate:=TS1*Tree_13.sieboldii.synRate;
161Tree_1.corrugata.synRate:=TS1*Tree_13.corrugata.synRate;
162Tree_1.iris.synRate:=TS1*Tree_13.iris.synRate;
163Tree_1.Node24.synRate:=TS1*Tree_13.Node24.synRate;
164Tree_1.Node21.synRate:=TS1*Tree_13.Node21.synRate;
165Tree_1.Node27.synRate:=TS1*Tree_13.Node27.synRate;
166
167END;
168