#NEXUS 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; end;