begin data;
[!Primate mtDNA data from: Hayasaka, K., T. Gojobori, and
S. Horai. 1988. Molecular phylogeny and evolution of primate
mitochondrial DNA. Mol. Biol. Evol., 5:626-644.]
dimensions ntax=12 nchar=898;
format datatype=dna interleave gap=-;
matrix
Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCT
Pan AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCT
Gorilla AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCAT
Pongo AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCT
Hylobates AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTT
Macaca_fuscata AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTT
M._mulatta AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTT
M._fascicularis AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTT
M._sylvanus AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTT
Saimiri_sciureus AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGT
Tarsius_syrichta AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCT
Lemur_catta AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCAT
Homo_sapiens CATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGC
Pan CATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGC
Gorilla CATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGC
Pongo CCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGC
Hylobates CCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGC
Macaca_fuscata CCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGT
M._mulatta CCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGT
M._fascicularis CCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGT
M._sylvanus CCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGC
Saimiri_sciureus CTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGA
Tarsius_syrichta CCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGA
Lemur_catta CCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGT
Homo_sapiens ATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTT
Pan ATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTT
Gorilla ATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCT
Pongo ATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCT
Hylobates ATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTT
Macaca_fuscata ACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTT
M._mulatta ACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTT
M._fascicularis ACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTT
M._sylvanus ATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTT
Saimiri_sciureus ACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCT
Tarsius_syrichta ACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAAC
Lemur_catta ACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCAC
Homo_sapiens TTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTA
Pan TTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTA
Gorilla TTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTA
Pongo CTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCA
Hylobates CTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTA
Macaca_fuscata TTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCA
M._mulatta CTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCA
M._fascicularis CTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTA
M._sylvanus CTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTA
Saimiri_sciureus CTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTA
Tarsius_syrichta ATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTA
Lemur_catta CTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCA
Homo_sapiens ACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAAT
Pan ATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAAT
Gorilla ACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAAC
Pongo ACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAAC
Hylobates ACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAAC
Macaca_fuscata ATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCAT
M._mulatta ACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCAT
M._fascicularis ATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCAT
M._sylvanus ATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCAC
Saimiri_sciureus ATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAAC
Tarsius_syrichta ATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACAC
Lemur_catta ATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAAC
Homo_sapiens ATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTC
Pan ACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTC
Gorilla ACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTC
Pongo ATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTC
Hylobates ACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTC
Macaca_fuscata ATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTC
M._mulatta ATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTC
M._fascicularis ATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTC
M._sylvanus ATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTC
Saimiri_sciureus TTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTC
Tarsius_syrichta CTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTC
Lemur_catta ATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTC
Homo_sapiens CCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTA
Pan CCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTA
Gorilla CCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCA
Pongo TCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCA
Hylobates CCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTA
Macaca_fuscata TCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAA
M._mulatta CCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAA
M._fascicularis TCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAA
M._sylvanus TCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAA
Saimiri_sciureus ACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCA
Tarsius_syrichta CCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCA
Lemur_catta CCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGC
Homo_sapiens ACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACAC
Pan ATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACAC
Gorilla CCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCAC
Pongo ACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACAC
Hylobates AAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCAC
Macaca_fuscata TCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACAC
M._mulatta TCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACAC
M._fascicularis TCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACAC
M._sylvanus TTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACAC
Saimiri_sciureus GCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACAT
Tarsius_syrichta ACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACAC
Lemur_catta ACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACAC
Homo_sapiens CTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTT
Pan CTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATT
Gorilla CTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTT
Pongo CTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTT
Hylobates CTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTT
Macaca_fuscata CTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTT
M._mulatta CTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTT
M._fascicularis CTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTT
M._sylvanus CTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATT
Saimiri_sciureus ATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACC
Tarsius_syrichta CTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAAC
Lemur_catta ATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACC
Homo_sapiens TTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACA
Pan CACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACA
Gorilla CACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATA
Pongo CGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATA
Hylobates TACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACA
Macaca_fuscata TACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACC
M._mulatta TACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACC
M._fascicularis TACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACT
M._sylvanus TACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACT
Saimiri_sciureus CTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATA
Tarsius_syrichta CATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATA
Lemur_catta CACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAA
Homo_sapiens ACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGC
Pan ACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGC
Gorilla ACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGC
Pongo ATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGC
Hylobates ATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGC
Macaca_fuscata ATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGC
M._mulatta ATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGC
M._fascicularis ATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGC
M._sylvanus ATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGC
Saimiri_sciureus ATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGC
Tarsius_syrichta ATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGC
Lemur_catta ATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGC
Homo_sapiens TAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGA
Pan TAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGA
Gorilla TAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGA
Pongo TAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGA
Hylobates TAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGA
Macaca_fuscata TAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA
M._mulatta TAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA
M._fascicularis TAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGA
M._sylvanus TAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGA
Saimiri_sciureus TAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGA
Tarsius_syrichta TAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGA
Lemur_catta TAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGA
Homo_sapiens TAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAA
Pan TAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAA
Gorilla TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAA
Pongo TAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAA
Hylobates TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAA
Macaca_fuscata TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAA
M._mulatta TAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAA
M._fascicularis TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAA
M._sylvanus TAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAA
Saimiri_sciureus TAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAA
Tarsius_syrichta TAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAA
Lemur_catta TAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAA
Homo_sapiens ATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTC
Pan ATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCC
Gorilla ATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTC
Pongo ATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTC
Hylobates ATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTC
Macaca_fuscata ATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTC
M._mulatta ATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTC
M._fascicularis ATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTC
M._sylvanus ATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTC
Saimiri_sciureus ATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAG
Tarsius_syrichta ATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACT
Lemur_catta ATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTAT
Homo_sapiens CCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACT
Pan CTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACT
Gorilla CTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCT
Pongo CCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACC
Hylobates CCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACT
Macaca_fuscata CCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTC
M._mulatta CCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTC
M._fascicularis CCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTT
M._sylvanus CCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACC
Saimiri_sciureus CCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACAC
Tarsius_syrichta CTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATG
Lemur_catta CCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACC
Homo_sapiens CATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGT
Pan CATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGC
Gorilla CATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGC
Pongo CATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGC
Hylobates TATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGC
Macaca_fuscata CATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGC
M._mulatta CATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGC
M._fascicularis CATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGT
M._sylvanus TATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGC
Saimiri_sciureus TATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGT
Tarsius_syrichta CATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGC
Lemur_catta CCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGC
Homo_sapiens CTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTC
Pan CTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTC
Gorilla CTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTC
Pongo CTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCAC
Hylobates CTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTC
Macaca_fuscata CTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTG
M._mulatta CTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTG
M._fascicularis CTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTG
M._sylvanus CTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTG
Saimiri_sciureus ACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTC
Tarsius_syrichta CTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTC
Lemur_catta CTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTC
Homo_sapiens GAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT
Pan AAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT
Gorilla AAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT
Pongo AAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT
Hylobates AAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT
Macaca_fuscata GAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT
M._mulatta AAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT
M._fascicularis GAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT
M._sylvanus AAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT
Saimiri_sciureus AAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT
Tarsius_syrichta CAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT
Lemur_catta CAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT
;
end;
begin assumptions;
usertype ttbias2
stepmatrix = 4
A C G T
[A] . 2 1 2
[C] 2 . 2 1
[G] 1 2 . 2
[T] 2 1 2 . ;
usertype ttbias6
stepmatrix = 4
A C G T
[A] . 6 1 6
[C] 6 . 6 1
[G] 1 6 . 6
[T] 6 1 6 . ;
usertype tvonly
stepmatrix = 4
A C G T
[A] . 1 0 1
[C] 1 . 1 0
[G] 0 1 . 1
[T] 1 0 1 . ;
charset tRNA_His = 459-528;
charset 'tRNA_Ser_(AGY)' = 529-588;
charset 'tRNA_Leu_(CUN)' = 589-659;
charset 1st_positions = 2-455\3 660-894\3;
charset 2nd_positions = 3-456\3 661-895\3;
charset 3rd_positions = 4-457\3 662-896\3;
exset protein_only = 1 458-659 897 898;
exset non_protein = 2-457 660-896;
end;
begin codons;
codonposset * codons = N: 1 458-659 897 898, 1: 2-455\3 660-894\3,
2: 3-456\3 661-895\3, 3: 4-457\3 662-896\3;
;[temp]codeset * codeset = mtDNA.mam.ext: all;
end;
begin sets;
charset Non = 1 458-659 897 898;
charset 1st = 2-455\3 660-894\3;
charset 2nd = 3-456\3 661-895\3;
charset 3rd = 4-457\3 662-896\3;
charpartition *a = n3:Non 3rd, 1:1st, 2:2nd;