#NEXUS [written Thu Dec 21 22:16:23 WIT 2017 by Mesquite version 3.3 (build 854) at NoPsechrids/192.168.1.118] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=51; TAXLABELS Rana_japonica_Raja01 Rana_japonica_Raja02 Rana_japonica_Raja03 Rana_japonica_Raja04 Rana_japonica_Raja05 Rana_japonica_Raja06 Rana_japonica_Raja07 Rana_japonica_Raja08 Rana_japonica_Raja09 Rana_ornativentris_Raor01 Rana_ornativentris_Raor02 Rana_ornativentris_Raor03 Rana_ornativentris_Raor04 Rana_ornativentris_Raor05 Rana_ornativentris_Raor06 Rana_ornativentris_Raor07 Rana_ornativentris_Raor08 Rana_ornativentris_Raor09 Rana_ornativentris_Raor10 Rana_ornativentris_Raor11 Rana_tagoi_Rata01 Rana_tagoi_Rata02 Rana_tagoi_Rata03 Rana_tagoi_Rata04 Rana_tagoi_Rata05 Rana_tagoi_Rata06 Rana_tagoi_Rata07 Rana_tagoi_Rata08 Rana_tagoi_Rata09 Rana_tagoi_Rata10 Rana_tagoi_Rata11 Rana_tagoi_Rata12 Rana_tagoi_Rata13 Rana_pirica_Rapitr1 Rana_pirica_Rapitr2 Rana_pirica_Rapitr3 Altirana_parkeri_NapaDRB1XM018558121 Xenopus_tropicalis_XetrNM001045794 Xenopus_laevis_XelaD13684 Xenopus_laevis_XelaD13688 Ambystoma_tigrinum_AmtiDAB0701DQ125480 Ambystoma_davidianus_AndaDAB0501KF611886 Ambystoma_mexicanum_AmmeDABB1021AF209115 Homo_sapiens_HosaDQBM33907 Rhinella_marina_RhmaDAB01KP995700 Rhinella_marina_RhmaDBB01KP995704 Rhinella_marina_RhmaDCB01KP995706 Quasipaa_spinosa_QuspKJ082083 Rana_catesbeiana_LicaBT081564 Rana_catesbeiana_Licatr1 Rana_catesbeiana_Licatr2 ; END; BEGIN CHARACTERS; TITLE Rana_MHCII_exon2; DIMENSIONS NCHAR=289; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Rana_japonica_Raja01 AGAGCAGAACCCGCCGATTATGTTCTTGAAGGGAAGGATGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTATCTGCGCAAATATTTCTACAATGAGGAGGAGTTTGTATACTTTGACAGCGATGTCGGATATTATATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGACCTCATAGAAGAACAGAAGGCCTCGGTGCAGACATTCTGTATATACAACAATAAGGTATCTGAGAATGCGGGGGTCATAGGGAGGAGA- Rana_japonica_Raja02 AGAGCAGAACCCGCCGATTATGTTCTTGAAGGGAAGGATGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTATCTGCGCAAATATTTCTACAATGAGGAGGAGTTTGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGACCTCATAGAAGAACAGAAGGCCTCGGTGCAGACATTCTGTATATACAACAATAAGGTATCTGAGAATGCGGGGGTCATAGGGAGGAGA- Rana_japonica_Raja03 ACAGTAGAATCTGCCGATTATGTTATTGAAGCGAAGGCTGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTTTCTGAACAGATATTTCTACAATGAGGAGGAGGATTTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGAATCCAA---GCTGAATACTGGAACAAGAATAAGGACTACATAGAACAAAGAAAGGCCGCGGTGCAGACATTGTGTATACCCAACTATGGTACAGCTGAGAATTCGGGGATCCCAGGGAGGAGA- Rana_japonica_Raja04 ACAGTAGAATCTGCCGATTATGTTACTGAAGAGAAGGGTGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTATCTGGATAGATATTTCTACAATGAGGAGGAGTTTGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCGGAATACTGGAACAAGAATAAGGACATCATAGAACAAAAAAAGGCCGAGCTGCAGACATTCTGTATACACAACTATGGTACAGCTGAGACTGTGGGGATCCCAGGGAGGAGA- Rana_japonica_Raja05 ACAGTAGAATCTGCCGATTATGTTACTGAAGAGAAGGGTGAATGTCACTACATGAACGGCACTCAGAGGGTGAAGTATCTGGATAGATATTTCTACAATGAGGAGGAGTTTGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCGGAATACTGGAACAAGAATAAGGACATCATAGAACAAAAAAAGGCCGAGCTGCAGACATTCTGTATACACAACTATGGTACAGCTGAGACTGTGGGGATCCCAGGGAGGAGA- Rana_japonica_Raja06 ACAGTAGAATCTGCCGATTATGTTACTGAAGAGAAGGGTGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTATCTGGATAGATATTTCTACAATGAGGAGGAGTTTGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCGGAATACTGGAACAAGAATAAGGACATCATAGAACAAAAAAAGGCCGAGCTGCAGACATTCTGTATACACAACTATGGTACAGCTGAGACTGTGGGGATCCCAGGGAGGAGA- Rana_japonica_Raja07 ACAGTAGAATCTGCCGATTATGTTATTGAACAGAAGGCTGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTTTCTGAACAGATATTTCTACAATGAGGAGGAGGATTTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGAATCCAA---GCTGAATACTGGAACAAGAATAAGGACTACATAGAACAAAGAAAGGCCGCGGTGCAGACATTGTGTATACCCAACTATGGTACAGCTGAGAATTCGGGGATCCCAGGGAGGAGA- Rana_japonica_Raja08 AGAGCAGAACCCGCCGATTATGTTCTTGAAGGGAAGGATGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTATCTGCGCAAATATTTCTACAATGAGGAGGAGTTTGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCTGAT---GCTGAATACTGGAACAAGAATAAGGACCTCATAGAAGAACAGAAGGCCTCGGTGCAGACATTCTGTATATACAACAATAAGGTATCTGAGAATGCGGGGGTCATAGGGAGGAGA- Rana_japonica_Raja09 ACAGTAGAATCTGCCGATTATGTTATTGAACAGAAGGCTGAATGTCACTACATGAACGGCACTCAGAGGGTGAGGTTTCTGAACAGATATTTCTACAATGAGGAGGAGGATTTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGAATCCAA---GCTGAATACTGGAACAAGAATAAGGACTACATAGAACAAAGAAAGGCCGCGGTGCTGACATTGTGTATACCCAACTATGGTACAGCTGAGAATTCGGGGATCCCAGGGAGGAGA- Rana_ornativentris_Raor01 ACAGTAGAATCTGCCGATTATGTTATTGAAGGGAAGGCTGAATGTCACTATATGAACGGCACTCAGAGGGTGAGGCTTCTTGAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGCGATGTCGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGCT---GCTGAAAACTGGAACAAGAATAAGGACATCATAGAACAAAGAAAGGCCGAGATGCAGACATTCTGTATATATAACTATGGGGCATTTGAGACTGTGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor02 ACAGTAGAATCTGCCGATTATGTTATTGAAGGGAAGGCTGAATGTCACTATATGAACGGCACTCAGAGGGTGAGGCTTCTTGAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGCGATGTTGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGCT---GCTGAAAACTGGAACAAGAATAAGGACATCATAGAACAAAGAAAGGCCGAGATGCAGACATTCTGTATATATAACTATGGGGCATTTGAGACTGTGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor03 ACAGTAGAATCTGCCGATTATGTTATTGAAGGGAAGGCTGAATGTCACTATATGAACGGCACTCAGAGGGTGAGGCTTCTTGAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGTGATGTTGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGCT---GCTGAAAACTGGAACAAGAATAAGGACATCATAGAACAAAGAAAGGCCGAGATGCAGACATTCTGTATATATAACTATGGGGCATTTGAGACTGTGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor04 AGAGCAGAACCCGCCGATTATGTTCTTGAAGGGAAGTTTGAATGTCATTATATGAACGGCACTCAGAGGGTGAGGCTTCTGCAGAGACTGTTCTACAATGAGGAGGAGTTTGTCTACTTTGACAGTGATGTCGGATATTTCATACCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGATTACATAGAACAACTGAAGGCCGCGGTGCAGACATTCTGTATACACAACTATGAGGTATCTGAGAATGCGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor05 ACAGTAGAATCTGCCGATTATGTTATTGAAGGGAAGGCTGAATGTCACTATATGAACGCCACTCAGAGGGTGAGGCTTCTTGAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGTGATGTTGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGCT---GCTGAAAACTGGAACAAGAATAAGGACATCATAGAACAAAGAAAGGCCGAGATGCAGACATTCTGTATATATAACTATGGGGCATTTGAGACTGTGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor06 AGAGCAGAACCTGCTGATTATGTTTTTGAAGGGAAGGATGAATGTCACTATATGAACGCCACTCAGAGGGTGAAGTATCTGCGCAAATATTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGCGATGTCGGATATTTCATACCGAAGACGGAGTTCGGGAGACTCCAA---GCTGAAAACTGGAACAAGAATAAGGATTACATAGAACAACTGAAGGCCCAGGTGCAGACATTCTGTATACAGAACTATGAGGTATTTGAGACTATGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor07 ACAGTAGAAACTGCCGATTATGTTATTGAATCGAAGTTTGAATGTCACTATATGAACGGCACTCAGAAGGTGAGGTATCTGCACAGACTGTTCTACAATCAGGAGGAGATTGCATACTTTGACAGCGATAAGGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGAT---GCTGATTACTGGAACAAGGATAAGGACATCATAGAACGAAGAAAGGCCGCGGTGCAGACAATCTGTATACCCAACTATGGTGTATTTCACAGCATCACAGCT---GACCGGAGA- Rana_ornativentris_Raor08 ACAGTAGAATCTGCCGATTATGTTATTGAAGCGAAATCTGAATGTCACTTCATGAACGGCACTCAGAAGGTGAGGTTTCTGCAGAGATGGTTCTACAATCAGGAGGAGCAGGTCTACTTTGACAGTGATAAGGGATATTACATACCGAAGACGGAGTTCGGGAGAATTGAT---GCTGATTACTGGAACAAGAATAAGGATTACATAGAACAACAGAAGGCCGATGTGCAGAGATTCTGTATAAACAACTATGGTGTATTTCACAGCGTCACAGCT---GACCGGAGA- Rana_ornativentris_Raor09 ACAGTAGAATCTGCCGATTATGTTATTGAAGGGAAGGCTGAATGTCACTATATGAACGGCACTCAGAGGGTGAGGCTTCTTGAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGTGATGTTGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGCT---GCTGAAAACTGGAACAAGAATAAGGACATCATAGAACAAAGAAAGGCCGAGATGCAGACATTCTGTATATATAACTATGGGGCATTTGAGACTGTGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor10 ACAGTAGAATCTGCCGATTATGTTATTGAAGGGAAGGCTGAATGTCACTATATGAACGCCACTCAGAGGGTGAGGTATCTTGAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGTGATGTTGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGCT---GCTGAAAACTGGAACAAGAATAAGGACATCATAGAACAAAGAAAGGCCGAGATGCAGACATTCTGTATATATAACTATGGGGCATTTGAGACTGTGGGGATCACAGGGAGGAGA- Rana_ornativentris_Raor11 ACAGTAGAATCCGCCGATTATGTTATTGAAATGAAGAGTGAATGTCACTATATGAACGGAACTCAGAAGGTGAGGTTTCTTGAGAGACTGTTCTACAATGAGGAGGAGCAGCTCTACTTTGACAGTGATAAGGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGATTACATAGAACAAAGAAAGGCCGCGGTGCAGACATACTGTATACCCAACTATGGGGTATCTGAGAATGCGGGGATCACAGGGAGGAGA- Rana_tagoi_Rata01 CCATTG---TCCGTGGATTACGTGTTTACATATAGGGGTGAATGTCACTATATGAACGGCACTCAGAAGGTGAGGAGTCTGGATAGATATTTCTACAATCAGGAGGAGTTTGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACAGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGATTTCATAGAACAACTGAAGGCCGAAGTGCAGGCAATCTGTATACCCAACTATGGTACAGCTGAGAATTCGGGGATCCCAGGGAGGAGA- Rana_tagoi_Rata02 ACAGTAGAATCTGCCGATTATGTTATGGAAGCGAAGTCTGAATGTCACTATATGAACGGCACTCAGAAGGTGAGGTTTCTGCAGAGATGGTTCTACAATCAGGAGGAGCAGCTCTACTTTGACAGCGATAAGGGATATTACATAGCGAAGACAGAGTTCGGGAGAATTGAT---GCTGATTACTGGAACAAGAATAAGGATTACATAGAACAACAGAAGGCCGATGTGCAGAGATTCTGTATAAACAACTATGGTGTATTTCACAGCGTCACAGCT---GACCGGAGA- Rana_tagoi_Rata03 AGAGCAGAATCTGCCGATTATGTTATTGAAGCGAAGAGTGAATGTCACTATATGAACGCCACTCAGAGGGTGAGGTATCTGCAGAGACATTTCTACAATGAGGAGGAGATTGTCTACTTTGACAGCGATGTCGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGACTTCATAGAACAACTGAAGGCCCAGGTGCAGACATTCTGTATACCCAACTATGAGGTATCTGAGAATGTGGGGATCACAGGGAGGAGA- Rana_tagoi_Rata04 ACAGTAGAATCTGCCGATTATGTTATTGAAGGGAAGGCTGAATGTCACTATATGAACGGCACTCAGAGGGTGAGGCTTCTTGAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGTGATGTTGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGCT---GCTGAAAACTGGAACAAGAATAAGGACATCATAGAACAAAGAAAGGCCGAGATGCAGACATTCTGTATATATAACTATGGGGCATTTGAGACTGTGGGGATCACAGGGAGGAGA- Rana_tagoi_Rata05 ACAGTAGAAACTGCCGATTATGTTATTGAATCGAAGTTTGAATGTCACTTCATGAACGGCACTCAGAAGGTGAGGTATCTGCACAGACTGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGCGATAAGGGATATTACATACCGAAGACGGAGTTCGGGAGACCCTCT---GCTGAATACTGGAACAAGAATAAGGACTTCATAGAACAAAGAAAGGCCGCGGTGCAGACAATCTGTATACCCAACTATGGTGTATTTCACAGCATCACAGCT---GACCGGAGA- Rana_tagoi_Rata06 ACAGTAGAATCTGCCGATTATGTTATTGAAGAGAAGTTTGAATGTCACTTCATGAACGGCACTCAGAAGGTGAGGCTTCTGGATAGATGGTTCTACAATCAGGAGGAGTTTGTATACTTTGACAGCGATAAGGGATATTACATACCGAAGACGGAGTACGGGAGACCCGAT---GCTGATTACTGGAACAAGGATAAGGACCTCATAGAACAAAGAAAGGCCTATGTGCAGACATACTGTATACACAACTATGATATCCTACACAGCGTCACAGCT---GACCGGAGA- Rana_tagoi_Rata07 ACAGTAGAATCTGCCGATTATGTTATTGAAGCGAAGTCTGAATGTCACTATATGAACGGCACTCAGAAGGTGAGGTTTCTGCAGAGATGGTTCTACAATCAGGAGGAGCAGTTCTACTTTGACAGCGATAAGGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTTCAACAAGGATAAGGATTACATAGAACAACAGAAGGCCGATGTGCAGAGATTCTGTATAAACAACTATGATGGCTTACACAGCGTCACAGCT---GACCGGAGA- Rana_tagoi_Rata08 ACAGTAGAATCTGCCGATTATGTTCTTGAAGAGAAGTCTGAATGTCACTATATGAACGGCACTCAGAGGGTGAGGTTTCTGCGCAGAGAATTCTACAATCAGGAGGAGCAGGTCTACTTTGACAGTGATAAGGGATATTTCATACCGAAGACGGAGTACGGGAGACCCGAT---GCTGAATACTGGAACAAGGATAAGGATTACATAGAACAACTGAAGGCCGTGGTGCAGACAATCTGTATACCCAACTATGAGGTATCTGAGAATGTGGGGATCCCAGGAAGGAGA- Rana_tagoi_Rata09 ACAGTAGAAACTGCCGATTATGTTACTGAAAATAAGGCTGAATGTCACTATATGAACGGCACTCAGAAGGTGAGGTATCTGGAGAGATATTTCTACAATCAGGAGGAGATTGTCTACTTTGACAGTGATAAGGGATATTTCATACCGAAGACGGAGTTCGGGAGAATTGAT---GCTGAATCCTGGAACAAGAATAAGGACTTCATAGAACAAAGAAAGGCCGCGGTGCAGACATTCTGTATACACAACTATGGTGTATTTCACAGCGTCACAGCT---GACCGGAGA- Rana_tagoi_Rata10 ACAGTAGAATCTGCCGATTATGTTATTGAAGAGAAGTTTGAATGTCACTTCATGAACGGCACTCAGAAGGTGAGGCTTCTGGATAGATGGTTCTACAATCAGGAGGAGATTGCATACTTTGACAGCGATAAGGGATATTACATACCGAAGACGGAGTTCGGGAGACCCGAT---GCTGATTACTGGAACAAGGATAAGGACCTCATAGAACAAAGAAAGGCCTATGTGCAGACATACTGTATACACAACTATGATATCCTACACAGCGTCACAGCT---GACCGGAGA- Rana_tagoi_Rata11 ACAGTAGAAACTGCCGATTATGTTATTGAATCGAAGTTTGAATGTCACTTCATGAACGGCACTCAGAAGGTGAGGTATCTGCACAGACTGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGCGATAAGGGATATTACATACCGAAGACGGAGTTCGGGAGACCCTCT---GCTGAATACTGGAACAAGAATAAGGATTTCATAGAACAAAGAAAGGCCGCGGTGCAGACAATCTGTATACCCAACTATGGTGTATTTCACAGCATCACAGCT---GACCGGAGA- Rana_tagoi_Rata12 ACAGTAGAAACTGCCGATTATGTTACTGAACAGAAGTCTGAATGTCACTTCATGAACGGCACTCAGAGGGTGAGGTATCTGCAGAGATGGTTCTACAATCAGGAGGAGTTTGTCTACTTTGACAGCGATAAGGGATATTTCATACCGAAGACAGAGTTCGGGAGACCCACT---GCTGAATACTGGAACAAGGATAAGGACATCATAGAACAAAGAAAGGCCGCGGTGCAGAGATTCTGTATACACAACTATGATGTATTTGAGACTCTGGGGATCCAAGGGAGGAGA- Rana_tagoi_Rata13 ACAGTAGAATCTGCCGATTATGTTATTGAAGCGAAGTCTGAATGTCACTATATGAACGGCACTCAGAAGGTGAGGTATCTGCAGAGATGGTTCTACAATCAGGAGGAGCAGTTCTACTTTGACAGTGATAAGGGATATTTCATACCGAAGACGGAGTTCGGGAGACACGAT---GCTGAATACTTAAACAAGGATAAGGATTACATAGAACAAAGAAAGGCCGCGGTGCAGACATTCTGTATACCCGACTATGATATCCTACACAGCGTCACAGCT---GACCGGAGA- Rana_pirica_Rapitr1 GTGCAGTAATCTGCCGATTATGTTACTGAAGGGAAGGCTGAATGTCACTTCATGAACGGCACTCAGAGGGTGAGGTTTCTGGAGAGATATTTCTACAATCAGGAGGAGTATGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGACCTCATAGAACAATACAAGGCCGCGGTGCAGACATACTGTATACCCAACTATGGTGGCCTACACGGCGTCACAGCT---GACCGGAGA- Rana_pirica_Rapitr2 ACAGTAGAATCTGCCGATTATGTTATTGAAGCGAAGTCTGAATGTCACTTCATGAACGGCACTCAGAGGGTGAAGTTACTGTACAGAAAGTTGTACAATCAGGAGGAGTATGTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCGTA---GCTGAATACTATAACAAGAATAAGGACATCATAGAACAATACAAGGCCTATGTGCAGACATTCTGTATACACAACTATGATATCATACACGGCGTCACAGCT---GACCGGAGA- Rana_pirica_Rapitr3 GTGCAGTAATCTGCCGATTATGTTACTGAAGTGAAGTTTGAATGTCACTTCATGAACGGCACTCAGAGGGTGAGGTATCTGGCGAGAGACTTCTACAATCAGGAGGAGGATTTATACTTTGACAGCGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAAGCCTGGAACAAGGATAAGGACATCATAGAACAACACAAGGCCTATGTGCAGACATTCTGTATACACAACTATGATATCATACACGGCGTCACAGCT---GACCGGAGA- Altirana_parkeri_NapaDRB1XM018558121 ---------TCCGCCGATTATGTTGTTGAAATGAAGTCTGAATGTCACTTCAGGAACGGCACTCAGAGGGTGAAGTTTCTTGACAGATATTTCTACAATCAGGAGGAGTCCGTCTACTTTGACAGCGATGTCGGAGATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAC---GCCGAATACTGGAACAAGGATAAGGATTTCATAGAACAAACAAGGGCCGCAGTGCAGACATTCTGTGTACACAACTATGGTGTCCTACACAGTGTCACTGCT---GACCGGAGA- Xenopus_tropicalis_XetrNM001045794 TCCTCACCTCCAGAGGATTTCGTGTATCAGTACAAGGGTCAGTGTTGCTTCAGGAACGGCACCGAGAATGTCAGGGGTCTGGATCGCTACATATATAACCAGGAGGAGATTGCGTACTTTGACAGCGATGTGGGTTTCTTTATCGCTAAAACCGAGCTGGGGAAAAAGCATTTCGCGGATTATTGGAACAGCCAGAAGGATCTCCTAGAGCAGAAACGGGCTGAGACGGATACAGTCTGCAGATACAACTATCAGTTTGATAAACCC---GATGTTATAGACAGGAAA- Xenopus_laevis_XelaD13684 TACTCACTCCCAGAGGATTACGTGTTTCAGTGGAAGAGTCAGTGTTACTACAGGAACGGCACCGACAATGTCAGGTATCTGGAAGGCTACGCTAATAATCAGGAGGAGTACGCCTACTTTGACAGTGATGTGGGGGAATATAAAGCTAAAAACGATTTTGGAGAAGTGCAG---GCGAAGTATTGGAACAGCCAGAAGGATCTCCTAGATCAGAAACGGGCTGTGGTGGATACAGTCTGCAGATACAACTATCAGCTATATAAACCC---TACACTGTAGACAGGAAA- Xenopus_laevis_XelaD13688 TCCTCCCCCCCAGAGGATTTCGTGTATCAGTTCAAGGGTCAGTGTTACTACAGGAACGGCACCGACAATGTCAGGCTTCTGTGGCGCCACTACTATAACCTGGAAGAAACCGATTACTTTGACAGTGATGTGGGTTTGTTTATCGCTAAAACCGAGCTGGGGAAACCGGAT---GCGGATAATTGGAACAGCCAGAAGGATTTCCTAGAGCAGACACGGGCTGCGGTGGACACAGTCTGCAGACACAACTATCAGATCGATAAACCC---TACACTATAGACAGGAAA- Ambystoma_tigrinum_AmtiDAB0701DQ125480 AGAGAGACCCCAGATGATTTCGTGACTCAGGTGAAGCACGAGTGCCACTTCCTGAACGGCTCGGAGCGGGTGCGCTATGTGGTGCGCTTTTCCTACAACCAGCAGCCGTTCGTGCACTTCGACAGCGACACGGGGGTCTTCCAGGCGGACACTCCCTTCGGGGTCCCGGAC---GCCAAGTACTGGAACAGCCAGAAGGAGGTCCTGGAGCAGGCGAGGGCCGAGGTGGACACGTTCTGCAGATTCAACTACGGGATCTTTGAAGAC---TTCATGCAGCGCCGCAGA- Ambystoma_davidianus_AndaDAB0501KF611886 GGCACAGCGCCAGCGGATTTCGTGGCACAGTATAAGGCCGAGTGTCACTTCCCGGACGGCTCGGAGCGGGTGCGCTTCCTGGACCGCTATTTCTACAACCAGGAGGAGTTCGTGTATTTTGACAGCGATGTCGGGCGCTATGTCCCGAAAACCGAGTTCGGGAAAACGACC---GCGGATTATTGGAACAACGACCAGGCCTTCCTGGAGCAGAAGAAGGCCGAGGTGGAGAGAGTCTGCAAACACAACTATGACGTGCGTAAACAA---GATGCCAGGAGCTGGAAA- Ambystoma_mexicanum_AmmeDABB1021AF209115 AGAGAGACCCCAGATGATTTCGTGACTCAGTGGAAGTCCGAGTGCCACTTCCTGAACGGGACGGAGCGGGTGCGCTATGTGGCGCGATGGTCCTACAATCAGCAGCAGTTCCTGCACTTCGACAGCGACACGGGGGTCTTCAAGGCGGACGACCTCCTCGGGGTCCCGAGC---GCCGAGTCCTTGAACAGCCAGAAGGAGGTCCTGGAGCAGGAGAGGGCCGCGGTGGACACGTTCTGCAGACACAACTACGGGATCTTGGAAGAC---TTCATGCAGCGCCGCAGA- Homo_sapiens_HosaDQBM33907 AGAGACTCTCCCGAGGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGGACCGAGCGCGTGCGGGGTGTGACCAGATACATCTATAACCGAGAGGAGTACGCGCGCTTCGACAGCGACGTGGGGGTGTATCGGGCGGTGACGCCGCTGGGGCGGCTTGAC---GCCGAGTACTGGAATAGCCAGAAGGACATCCTGGAGGAGGACCGGGCGTCGGTGGACACCGTATGCAGACACAACTACCAGTTGGAGCTCCGC---ACGACCTTGCAGCGGCGA- Rhinella_marina_RhmaDAB01KP995700 TCGTCAGCTGCTGTGGATTACATGACTGAACAGAAGGCAGAATGTCACTATGTGAACGGGACTCAGCAGGTGCGGTATCTGGACAGATATTTCTACAATCAGGAGGAGTTTGTTTACTTTGACAGCGATAAGGGATATTTCATAGCGAAGACTGAGTTCGGGAAACCAGAT---GCAGATTACTGGAACAAGAATAAGGATATCATAGAAGACGAGAAGAGCGCAGTGGAGACATACTGTATACCTAACTATGGAGTGTGGAAA---GAAGGAGCTATAGAAAGAAAA- Rhinella_marina_RhmaDBB01KP995704 TCATCGGACTTCAGAGATTACGTACTAGCAGCAACCAGTGAATGTCACTATGTAAATGGGACTCAGCAGGTGCGGTTTCTGGACAGATATTTCTACAATCAGGAGGAGACCGTTTACTTTGACAGCGAGAAAGGATATTTCATAGCGAAGACTGAGCTCGGGAAACCGGAT---GCAGAACAATACAATAAGGATAAGGATTTCATAGAACAGAAGAAGAGCGCAGTGGAGACATACTGTAAACACAACTATGGAGTCATACACAGCGTCACTGCT---GACAGGAGA- Rhinella_marina_RhmaDCB01KP995706 TCATCGGATGTCAATGATTTTATAGAAGCAATAACCAGTGAATGTCACTATGTGAACGGGACTCAGCAGGTGCGGTATCTGGAGAGGTACATCTACAATCAGGAGGTGTATGTTTACTTTGACAGCGATGTCAGGTATTTTGTAGGGAAAGACGATTATGGGAGGATCAAT---GCCGATATCTGGAACAAGGATAAGAATTTCATAGAACAGAGGAGGACCGCGATGGAGATATTTTGTAGACCCAATTATGAATTACTCACATCTATGGGAATATCAGGGAGGAAA- Quasipaa_spinosa_QuspKJ082083 ACCTCCCATCCAGATGATTTCGTGTATCAGTTTAGGGGTCAGTGTTATTACAGGAACGGTACGGAGGATATCCAGCTTCTGAAACGTTGGTTTTACAATCGGGAGGAGTATGTGTACTTCGACAGCGATAGAGGAATCTACATCGCCAAAACTGAGCTGGGGAGACCGGAC---GCTAAATACTGGAACAGCCAACCGGATGTATTGGCAGAAGCGCGGGCTGCGGTGGACAGAGTCTGCAGACACAACTATCAGATCTACAAACCT---GCAGCCATAGACCGGAAA- Rana_catesbeiana_LicaBT081564 TCACCGTTGTCCGTGGATTACGTGTATACAAGTAGAGGTGAATGTCACTTCATGAACGGCACTCAGAGGGTGAGGCTTCTGCACAGACATTTCTACAATGAGGAGGAGTTCGTATACTTTGACAGTGATGTCGGATATTTCATAGCGAAGACGGAGTTCGGGAGACCCTCT---GCTGAATACTGGAACAAGAATAAGGAGTACATAGAACAAAAAAAGGCCGAGGTGCAGACATACTGTATGCCCAACTATGATATCATACACAGC---GTCACTGCTGACCGGAGA- Rana_catesbeiana_Licatr1 TCACCGTTGTCCGTGGATTACGTGTTTACATTTAGAGGTGAATGTCAATTCATGAACGGCACTCAGAGGGTGAGGTTTCTGCAGAGACTATTCTACAATCAGGAGGAGCAGGTATACTTTGACAGTGATAAGGGATATTATATACCGAAGACGGAGTACGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGAGTACATAGAACAAATGAAGGCCGCGGTGCAGACAGTCTGTATACACAACTATGATATCCTACACAGC---GTCACTGCTGACCGGAGA- Rana_catesbeiana_Licatr2 AGAGCAGGACCCGCCGATTATATTATTGAAGGGAAGGATGAATGTCACTATATGAACGGCACTCAGAGGGTGAAGTATCTGCGGAGATATTTCTACAATCAGGAGGAGATCGTATACTTTGACAGTGATATCGGACATTTCATAGCGAAGACGGAGTTCGGGAGACCCGAT---GCTGAATACTGGAACAAGAATAAGGAGTACATAGAACAAATGAAGGCCGCGGTGCAGACAGTCTGTATACACAACTATGATATCCTACACAGC---GTCACTGCTGACCGGAGA- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 289; END; BEGIN NOTES; TAXABITS NAME = newlyAddedTaxon on = 1 - 51; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 289; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 289; END; BEGIN TREES; Title Rana_MHCII_exon2; ID 01607919f22f17; LINK Taxa = Taxa; TRANSLATE [0] 1 Rana_japonica_Raja01, [1] 2 Rana_japonica_Raja02, [2] 3 Rana_japonica_Raja03, [3] 4 Rana_japonica_Raja04, [4] 5 Rana_japonica_Raja05, [5] 6 Rana_japonica_Raja06, [6] 7 Rana_japonica_Raja07, [7] 8 Rana_japonica_Raja08, [8] 9 Rana_japonica_Raja09, [9] 10 Rana_ornativentris_Raor01, [10] 11 Rana_ornativentris_Raor02, [11] 12 Rana_ornativentris_Raor03, [12] 13 Rana_ornativentris_Raor04, [13] 14 Rana_ornativentris_Raor05, [14] 15 Rana_ornativentris_Raor06, [15] 16 Rana_ornativentris_Raor07, [16] 17 Rana_ornativentris_Raor08, [17] 18 Rana_ornativentris_Raor09, [18] 19 Rana_ornativentris_Raor10, [19] 20 Rana_ornativentris_Raor11, [20] 21 Rana_tagoi_Rata01, [21] 22 Rana_tagoi_Rata02, [22] 23 Rana_tagoi_Rata03, [23] 24 Rana_tagoi_Rata04, [24] 25 Rana_tagoi_Rata05, [25] 26 Rana_tagoi_Rata06, [26] 27 Rana_tagoi_Rata07, [27] 28 Rana_tagoi_Rata08, [28] 29 Rana_tagoi_Rata09, [29] 30 Rana_tagoi_Rata10, [30] 31 Rana_tagoi_Rata11, [31] 32 Rana_tagoi_Rata12, [32] 33 Rana_tagoi_Rata13, [33] 34 Rana_pirica_Rapitr1, [34] 35 Rana_pirica_Rapitr2, [35] 36 Rana_pirica_Rapitr3, [36] 37 Altirana_parkeri_NapaDRB1XM018558121, [37] 38 Xenopus_tropicalis_XetrNM001045794, [38] 39 Xenopus_laevis_XelaD13684, [39] 40 Xenopus_laevis_XelaD13688, [40] 41 Ambystoma_tigrinum_AmtiDAB0701DQ125480, [41] 42 Ambystoma_davidianus_AndaDAB0501KF611886, [42] 43 Ambystoma_mexicanum_AmmeDABB1021AF209115, [43] 44 Homo_sapiens_HosaDQBM33907, [44] 45 Rhinella_marina_RhmaDAB01KP995700, [45] 46 Rhinella_marina_RhmaDBB01KP995704, [46] 47 Rhinella_marina_RhmaDCB01KP995706, [47] 48 Quasipaa_spinosa_QuspKJ082083, [48] 49 Rana_catesbeiana_LicaBT081564, [49] 50 Rana_catesbeiana_Licatr1, [50] 51 Rana_catesbeiana_Licatr2; TREE Imported_tree_1 = (44:0.096477115,((41:0.05109154,43:0.05285111):0.09916046[%posteriorProbability = 1 ],((48:0.151674,(39:0.10213791,(38:0.0714254,40:0.075528):0.021518[%posteriorProbability = 0.934 ]):0.05173102[%posteriorProbability = 0.998 ]):0.02220651[%posteriorProbability = 0.835 ],(42:0.1597628,((45:0.09727561,(46:0.12350108,47:0.18115842):0.00945261[%posteriorProbability = 0.474 ]):0.01397528[%posteriorProbability = 0.62 ],(((51:0.0519026,(49:0.04985991,50:0.05408275):0.04845582[%posteriorProbability = 1 ]):0.0153308[%posteriorProbability = 0.668 ],(37:0.06488869,(35:0.05162771,(34:0.03045094,36:0.05198634):0.01468053[%posteriorProbability = 0.735 ]):0.0146812[%posteriorProbability = 0.846 ]):0.01453778[%posteriorProbability = 0.647 ]):0.00777194[%posteriorProbability = 0.27 ],((29:0.0456523,((16:0.02422977,(25:0.00116102,31:0.00242321):0.01519675[%posteriorProbability = 0.999 ]):0.02449736[%posteriorProbability = 0.976 ],((26:0.00443495,30:0.00631774):0.04694449[%posteriorProbability = 1 ],(33:0.03875927,(27:0.02657746,(17:0.01278138,22:0.01589245):0.01464117[%posteriorProbability = 0.98 ]):0.01321205[%posteriorProbability = 0.675 ]):0.01533149[%posteriorProbability = 0.893 ]):0.00372845[%posteriorProbability = 0.283 ]):0.00497494[%posteriorProbability = 0.333 ]):0.01965948[%posteriorProbability = 0.587 ],(((3:0.00249623,(7:0.0,9:0.00358685):0.00467222[%posteriorProbability = 0.931 ]):0.04900743[%posteriorProbability = 1 ],(21:0.09344594,(5:0.00307206,(4:0.0,6:0.0):0.00051217[%posteriorProbability = 0.768 ]):0.02613876[%posteriorProbability = 1 ]):0.00041695[%posteriorProbability = 0.17 ]):0.01316767[%posteriorProbability = 0.347 ],(((20:0.04608908,28:0.05426935):0.01163508[%posteriorProbability = 0.59 ],(23:0.03312673,(13:0.03852304,(15:0.0470515,(1:0.0055343,(2:0.00039692,8:0.00318731):0.00163416[%posteriorProbability = 0.767 ]):0.04972269[%posteriorProbability = 1 ]):0.00627983[%posteriorProbability = 0.563 ]):0.00002739[%posteriorProbability = 0.201 ]):0.01255847[%posteriorProbability = 0.534 ]):0.00650629[%posteriorProbability = 0.341 ],(32:0.04912223,(19:0.00532165,((10:0.00335311,11:0.00023112):0.00207197[%posteriorProbability = 0.374 ],(14:0.00261847,(12:0.0,(18:0.0,24:0.0):0.0[%posteriorProbability = 0.236 ]):0.00096575[%posteriorProbability = 0.483 ]):0.00102938[%posteriorProbability = 0.326 ]):0.00373221[%posteriorProbability = 0.435 ]):0.04377265[%posteriorProbability = 1 ]):0.01009009[%posteriorProbability = 0.556 ]):0.00350069[%posteriorProbability = 0.303 ]):0.02785366[%posteriorProbability = 0.605 ]):0.00902578[%posteriorProbability = 0.164 ]):0.03622911[%posteriorProbability = 0.99 ]):0.07412871[%posteriorProbability = 1 ]):0.01485637[%posteriorProbability = 0.753 ]):0.04163757[%posteriorProbability = 0.885 ]):0.096477115)[% ] [% ] [% setBetweenDouble = posteriorProbability ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1513862184827; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7605616739896563518; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2098734486485973648; mqVersion 330; checksumv 0 3 2658490282 null getNumChars 289 numChars 289 getNumTaxa 51 numTaxa 51 short true bits 15 states 15 sumSquaresStatesOnly 285963.0 sumSquares 285963.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 183; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1238 661; setLocation 36 58; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7605616739896563518 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 01607919f22f17; toggleUseWeights off; endTell; setAssignedID 3729.1513862103267.2616529875631272111; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1055 589; setLocation 36 58; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; toggleShowOnTerminals on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #2098734486485973648 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1055 589; setLocation 36 58; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; getEmployee #mesquite.charMatrices.AlterData.AlterData; tell It; toggleBySubmenus off; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 16 6 1 1; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;