kim.nex

功能强大的matlab写的bayes分类器

#NEXUS 
[This is an example of a model using a complex partitioned model, including a doublet partition and a partition
 analyzed using a codon model.]

[Data from Kim, S., K. M. Kjer, and C. N. Duckett. 2003. Comparison between molecular and 
    morphological-based phylogenies of galerucine/alticine leaf beetles 
    (Coleoptera: Chrysomelidae). Insect Syst. Evol. 34:53-64.]

begin data;
	dimensions ntax=27 nchar=1742;
	format datatype=mixed(rna:1-516,dna:517-1398,protein:1399-1692,standard:1693-1742) gap=- missing=? interleave=yes;
	matrix
	[                                                              1                  ]
	[                                                    11  1111  1111222  2222222333]
	[                                           12345678901  2345  6789012  3456789012]
	[                                           --------------------------------------]
	Orsodacne       [---------------kaCGu-CAG]  gGGUAAACCUN  AGaA  AcccnaA  AGGUCGAAUg
	Chrysomela      [-----------------CGUUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Altica          [------------------------]  -----------  ----  -CCCGAA  AGGUCGAAAG
	Agelastica      [----------------UUAUUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Monolepta       [---------CGUGAA-CCGUUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Phyllobrotica   [------------------------]  ---------UG  ANAA  ACCCGAA  AGGUCGAAAG
	Allochroma      [------------nUgaCCGUUCAg]  GGGUAAaCcUG  AgAA  aCCcGAA  AGGUCgAAAG
	Chrysolina      [-------------------UUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Aphthona        [AGUCAAGAGUACGUGACCGUUCAG]  GGGUAACCCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Chaetocnema     [------------------------]  -----------  ----  -CCCGAA  AGGUCGAAAG
	Systena         [------------------------]  ---CCGACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Monocesta       [------------------------]  ----------G  AGAA  ACCCGAA  AGGUCGAAAG
	Disonycha       [------------------------]  -----------  --AA  ACCCGAA  AGGUCGAAAG
	Blepharida      [------------------------]  -----------  ----  -CCCGAA  AGGUCGAAAG
	Galeruca        [--------------CAUCGUUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Orthaltica      [---------------ACCGUUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Paropsis        [-------------------UUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Timarcha        [------------------------]  -----AACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Zygograma       [------------UGAACCGUUCAG]  GGGUAAACCUG  AGAA  ACCCGAA  AGGUCGAAAG
	Syneta          [------------------------]  -----GAACUU  ACAA  ACCCGAA  AGGUCGAAAG
	Dibolia         [------aguacguaaaccguucag]  ggguaaaccug  agaa  acccgaa  aggucgaaag
	Sangariola      [------------------------]  -----------  ----  -CCCGAA  AGGUCGAAAG
	Aulacophora     [------------------------]  -----------  AGAA  ACCCGAA  AGGUCGAAAG
	Diabrotica      [---------------ACcGuUCA-]  GGGUAAACcUG  AgAA  ACCcGAA  AG-UCGAAAG
	Diorhabda       [------------------------]  -----------  AGAA  ACCCGAA  AGGUCGAAAG
	Schematiza      [------------------------]  -----????UG  AGAA  ACCCGAA  AGGUCGAAAG
	Oides           [--UCAAGAGUACGUGACCGUU-AG]  GGGUAACCCUG  AGAA  ACCCGAA  AGGUCGAAAG
		
	[               *2             2a          2b        2c                               2e       I1                I2              2ei                         2ci     2bi  2ai              2i*   ]
	[                                                                                                      1111 1111 111111111111111 1111  111111111111 1111111  11111   111  1111111  111111  111111]
	[               333333 344444  4444455  5  555  555  56666  66666677 77777 777888888  8888  99 999999990000 0000 001111111111222 2222  222333333333 3444444  44445   555  5555556  666666  666777]
	[               345678 901234  5678901  2  345  678  90123  45678901 23456 789012345  6789  01 234567890123 4567 890123456789012 3456  789012345678 9012345  67890   123  4567890  123456  789012]
	[               ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------]
	Orsodacne       gGGAAA UUCAuU  crCGUUU  C  NAA  --C  rUsgg  s-nc---- -CG-- ggUyraCgN  CGAG  AC GGGCN-CGCcg- UUcg Cr-CCAC-------G CUcg  CUCCGUCGUCC- GGCGCGC  CCGGC   GUC  GAACGCG  UGCACU  UUuCcC
	Chrysomela      GGGAAA UUCAUU  CGCGUUU  C  GUC  --U  GCCGG  C-GGUGAG -CG-- GGUGCGUGA  CGAA  CG GUG--------- UUCG ---CGCC-------G UUCG  CGCUGCUCGUUU UCUGGCA  CCGGU   GAC  GAACGCG  UGCACU  UUUCCC
	Altica          AGGAAA UUCAUU  CGCGUCU  C  GAC  --U  GUCGG  A-GUUGAA -AG-- UUUGUGUGA  CGGA  UU ACG--------- UUUA ---CGUC-------G UCCG  CGCCUCUCGUU- CUUCGAA  CCGAU   GUG  GAACGCG  UGCACU  UUUCCU
	Agelastica      AGGAAA UUCAUU  CGCGUUU  C  GAU  --C  GUCGA  A-GUCGAA -CG-- UUCGUAUGA  CGAA  CG ACGU-------- UUCG --GCGUC-------G UUUG  CUUCCUACGUU- UUUCUAA  UCGAU   GUC  GAACGCG  UGCACU  UUUCCU
	Monolepta       AGGAAA UUCAUU  CGCGUUU  C  GGC  ---  GUCGA  A-GUUAAG -CG-- UUUGUAUGA  CGAA  AG AUGU-------- UUCG --GCGUU-------U UUUG  CUUCUUACGUU- UUUCGAG  UCGAU   GUC  GAACGCG  UGCACU  UUUCCU
	Phyllobrotica   GGGAAA UUCAUU  CGCGUUU  C  GGC  --U  GUCGA  A-GUUGAA -UG-- UAUGUAUGA  CGGA  UG GCGU-------- UUCG --ACGUC-------G UCUG  CAUCUUGCGUU- CUUCAAG  UCGAU   GUC  GAACGCG  UGCACU  UUUCCU
	Allochroma      GGGAAA UUCaUU  CgCGUUU  C  GgC  --U  GUCGg  A-GUUGgA -UG-- UUCGUGUGA  CGgA  Ug ACG--------- UUCA ---CGUC-------G UUUG  CaCCUUACGUC- UUUCGAA  UCGAC   GUC  GAACGCG  UGCaCU  UUUCCU
	Chrysolina      GGGAAA UUCAUU  CGCGUUU  C  GAU  --C  GUUGG  C-GAUUGA -CG-- GACUAGUGA  CGGA  UG GCG--------- UUCG ---CGUC-------G UCUG  CGCAGUCUGUU- UAUCGAA  CUGAC   GUC  GAACGCG  UGCACU  UUUCCC
	Aphthona        GGGAAA UUCAUU  CGCGUUU  C  GGC  --C  GUCAG  A-GGU-GA -UG-- UUGU-GUGA  CGGA  UG GCG--------- UUCG ---CGUC-------G UCUG  CGCCUUGCGUC- CAUCUAA  CUGGC   GUC  GAACGCG  UGCACU  UUUCCC
	Chaetocnema     GGGAAA UUCAUU  CGCGUUU  C  GAC  --C  GUCGG  A-GUUGGA -CG-- UUCGAGUGA  CGGA  CG ACG--------- UUCG -CGCGUC-------G UCUG  CGCCGUUCGUU- CAUCGAA  CUGAC   GUC  GAACGCG  UGCACU  UUUCCC
	Systena         AGGAAA UUCAUU  CGCGUUU  C  GAU  UUU  GUCGG  A-GUUGAG -CG-- UUUCGGCGA  CGAA  UG ACG--------- UUUU AUAUGUC-------G UUUG  AGUCAUUCGUU- CUUCGAA  CCGAU   AUC  GAACGCG  UGCACU  UUUCCU
	Monocesta       AGGAAA UUCAUU  CGCGUUU  C  GAU  --C  GUCGA  AAGUUGAA -UGUA UUUGUAUGA  CGGA  UG ACGUGUGUGCGC UUCG GCUCUCUCAUGUUUA UCCG  CAUAUUAUAUU- CUUCGAA  UCGAU   AUC  GAACGCG  UGCACU  UUUCCU
	Disonycha       GGGAAA UUCAUU  CGCGUUU  C  GAU  --G  AUCGA  A-GGCUGG -CG-- UGUUUAUGA  CGGA  UC GUAUA------- ???? U---UUUUAUAUU-G UUCG  CAUAUCACGUU- CGUUUAA  UCGAU   UUC  GAACGCG  UGCACU  UUUCCU
	Blepharida      GGGAAA UUCAUU  CGCGUUU  C  AGC  --C  GUUGG  A-GUUGAA -CG-- UUCGCGUGA  CGGA  CG ACG--------- UUCG ---CGUC-------G UUUG  CGCCUUUCGUU- CUACUAA  CCGAC   GUU  GAACGCG  UGCACU  UUUCCU
	Galeruca        AGGAAA UUCAUU  CGCGUUU  C  GAU  --C  GUUGA  A-GUUGAA -UG-- UUUGUAUGA  CGGA  UG AUGU------GC UUCG --GCGC--AUGU--G UUUG  CAUCUUAUGUU- CUUCGAA  UCGAU   GUC  GAACGCG  UGCACU  UUUCCU
	Orthaltica      GGGAAA UUCAUU  CGCGUUU  C  GGC  --C  GUCGG  A-GUUGUG -CG-- UUCGUGUGA  CGGA  UG GCG--------- CUU- --GCGUC-------G UCCG  CGCCUUACGUG- CUUCGAA  CCGGC   GUC  GAACGCG  UGCACU  UUUCCU
	Paropsis        GGGAAA UUCAUU  CGCGUUU  C  GAC  --U  GUCGG  C-GAUAAG -UG-- AUCUAGUGA  CGGA  UG GCG--------- UUCG -CGCGUC-------G UCUG  CGCAGUUUAUU- UAUCGAA  CCGGC   GUC  GAACGCG  UGCACU  UUUCCU
	Timarcha        GGGAAA UUCAUU  CGCGUUU  C  GAU  --U  GUCGG  C-GAUAAA -CG-- AGCGAGUGA  CGGA  CG ACGU----ACG- UUCG -CGCGUAC--GUU-U UCUG  CUUCUUUCGUU- UAGGUAA  -CGAC   GCC  GAACGCC  UGCACU  UUUCCC
	Zygograma       GGGAAA UUCAUU  CGCGUUU  C  GGU  --C  GUCGG  C-UAUCGA -CG-- GGCUAGUGA  CGG-  UC GGCG-------- UUCG ---CGUC-------G UCUG  CGCAGUCUGUC- GAUUGAA  CCGAU   AUC  GAACGCG  UGCACU  UUUCCC
	Syneta          GGGAAA UUCAUU  CGCGUUU  C  GAC  --C  GUCGA  U-GACGAG -CG-- GUCGAGUGA  CGGA  UG GCG--------- UUCG ---CGUC-------G UCCG  CGCCUUCUGUU- CGUAGAA  UCGGC   GUC  GAACGCG  UGCACU  UUUCCC
	Dibolia         gggaaa uucauu  cgcguuu  c  ggc  -uc  gucgg  a-ggagaa -CG-- ucggcguga  cgga  ug acg--------- uucg -cgcguc-------g uucg  cacccuucguu- cuuuuua  ccggc   guc  gaacgug  ugcacu  uuuccu
	Sangariola      GGGAAA UUCAUU  CGCGUUU  C  GAC  --U  GUCGG  A-GUUGGA -CG-- UUCGAGUGA  CGGA  CG ACG--------- UUUG ---CGCG-------G UUUG  CGCCUUACGUU- UAUCGAA  CCGAC   GUC  GAACGCG  UGCACU  UUUCCU
	Aulacophora     GGGAAA UUCAUU  CCCUUUU  C  GGC  --U  GUCGA  C-GUUAAA -CG-- UUUAUACGA  CGGA  UG GCGU-------- UUCG --GCGUC-------G UCUG  CGUUUUAUGUU- UUUCGAA  UCGAU   GUC  GAACGCG  UGCACU  UUUCCU
	Diabrotica      AGgAAA UUCAUU  CGCGUUU  C  GAC  --U  GUCGA  A-GUUGGA -UG-- UUUGUAUGA  CGGA  UA GCGU-------- UUCG --GCGUC-------G UCCG  CUUCUUAUAUU- CUUCGUG  UCGAU   GUC  GAACGCG  UGCACU  UUUCCU
	Diorhabda       AGGAAA UUCAUU  CGCGUUU  C  GAU  --A  AUUGA  A-GUUGAA CCG-- UUUGUAUGA  CGGA  UA UUGU--UUGUGU UUCG GCAUAUUAC-AAUAA AUCG  CGUUUUACGUU- UUUCUAA  UCGAU   AUC  GAACGCG  UGCACU  UUUCCU
	Schematiza      GGGAAA UUCAUU  CGCGUUU  C  GAu  --C  GUCUA  C-GUUAAA -UG-- UUUGUAUGA  CGGA  UG AGAUA-CGUCG- UUCG CGGCGCCU----GAG UCCG  CAUCUUAUGUU- UAUCUAA  UAGAU   GUC  GAACGCG  UGCACU  UUUCCU
	Oides           GGGAAA UUCAUU  CGCGUUU  C  GAU  --U  GUUGA  U-AUCGAG -CA-- UUAGUAUGA  CGGU  AA aCGu-------- UUCG AUGu---------UU AUUG  CAUCUUUuGGU- CUUUuAA  UCGAU   AUC  GAACGCG  UGCACU  UUUCCU
	
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