#NEXUS [written Sat Mar 27 15:05:08 EDT 2010 by Mesquite version 2.7 (build 510) at ComPhy.local/10.0.1.3] BEGIN TAXA; TITLE 'Triops_haplotypes'; DIMENSIONS NTAX=32; TAXLABELS Triops_longicaudatus_AY639934_ Triops_granarius_AY115612_ Lepidurus_apus_apus__AY159584 Lepidurus_apus_lubbocki_AY159583 Lepidurus_arcticus_AY159585_ Lepidurus_lemmoni_AY115614_ Triops_cancriformis_cancriformis_1 Triops_cancriformis_cancriformis_2 Triops_cancriformis_cancriformis_8 Triops_cancriformis_cancriformis_5 Triops_cancriformis_cancriformis_3 Triops_cancriformis_cancriformis_4 Triops_cancriformis_cancriformis_6 Triops_cancriformis_cancriformis_7 Triops_mauritanicus_Gitanilla Triops_mauritanicus_Portugal Triops_mauritanicus_S_Iberia_1 Triops_mauritanicus_S_Iberia_2 Triops_mauritanicus_S_Iberia_3 Triops_mauritanicus_mauritanicus__7 Triops_mauritanicus_mauritanicus_1 Triops_mauritanicus_mauritanicus_2 Triops_mauritanicus_mauritanicus_3 Triops_mauritanicus_mauritanicus_4 Triops_mauritanicus_mauritanicus_5 Triops_mauritanicus_mauritanicus__6 Triops_mauritanicus_Cadiz_1 Triops_mauritanicus_Cadiz_2 Triops_mauritanicus_Cadiz_3 Triops_mauritanicus_simplex_3 Triops_mauritanicus_simplex_2 Triops_mauritanicus_simplex_1 ; END; BEGIN CHARACTERS; TITLE '16S_rRNA_alignment'; DIMENSIONS NCHAR=432; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = N; MATRIX Triops_longicaudatus_AY639934_ ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGGAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_granarius_AY115612_ ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Lepidurus_apus_apus__AY159584 ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAGTTTCTGTCTCTATCG Lepidurus_apus_lubbocki_AY159583 ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTCTTAATTGGAGGCTGGTATGAATGGCTGGACGAGAAAGTTTCTGTCTCTATTG Lepidurus_arcticus_AY159585_ ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTATCA Lepidurus_lemmoni_AY115614_ ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTATTG Triops_cancriformis_cancriformis_1 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_cancriformis_cancriformis_2 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_cancriformis_cancriformis_8 ATGGCCGCGGTATTCTGACCGTGCAAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_cancriformis_cancriformis_5 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_cancriformis_cancriformis_3 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_cancriformis_cancriformis_4 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTTAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_cancriformis_cancriformis_6 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_cancriformis_cancriformis_7 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_Gitanilla ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGGTA Triops_mauritanicus_Portugal ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_S_Iberia_1 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_S_Iberia_2 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_S_Iberia_3 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_mauritanicus__7 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_mauritanicus_1 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_mauritanicus_2 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_mauritanicus_3 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_mauritanicus_4 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_mauritanicus_5 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_mauritanicus__6 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_Cadiz_1 ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_Cadiz_2 ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_Cadiz_3 ATGGCCGCGGTATTTTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_simplex_3 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_simplex_2 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_mauritanicus_simplex_1 ATGGCCGCGGTATTCTGACCGTGCGAAGGTAGCATAATCATTAGTCTTTTAATTGAAGGCTGGTATGAATGGCTGGACGAGAAAATTTCTGTCTCTGTTA Triops_longicaudatus_AY639934_ TAAAATTCGAATTTTATTTTTAAGTGAAAAAGCTTAAATTTGTTTGAGGGACGATAAGACCCTATGGATCTTTATAATGATATATAGTAAAAAGCTTAGG Triops_granarius_AY115612_ TAATATTTGAATTTTATTTTTAAGTGAAAAAGCTTAAATTTTTTTGAGGGACGATAAGACCCTATGGATCTTTATAATAATAAATAGTAAAAAGCTTAGA Lepidurus_apus_apus__AY159584 TAAAGTTTGAATTTTATTTTTAAGTGAAAAAGCTTAAATAATTTTGAGGGACGATAAGACCCTATGGATCTTTATATAAATTTATAATAAAAAGTTTGGT Lepidurus_apus_lubbocki_AY159583 TAAAGTTTGAATTTTATTTTTAAGTGAAAAAGCTTAAATGTTTTTGAGGGACGATAAGACCCTATGGATCTTTATATGAATTAATGGTAAAAAGTCTAGT Lepidurus_arcticus_AY159585_ TAAAATTTGAATTTTATTTTTAAGTGAAAAAGCTTAAATAATTTTGAGGGACGATAAGACCCTATGGATCTTTATATGAATTTATAATAAAAAGATTGGA Lepidurus_lemmoni_AY115614_ TAAAATTTGAATTTTATTTTTAAGTGAAAAAGCTTAAATAATTTTGAGGGACGATAAGACCCTATGGATCTTTATATGAATTTATAATAAAAAGATTGGT Triops_cancriformis_cancriformis_1 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_cancriformis_cancriformis_2 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_cancriformis_cancriformis_8 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_cancriformis_cancriformis_5 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_cancriformis_cancriformis_3 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_cancriformis_cancriformis_4 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_cancriformis_cancriformis_6 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_cancriformis_cancriformis_7 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATGATGATTAATAAAAAGTTTAGA Triops_mauritanicus_Gitanilla TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_Portugal TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_S_Iberia_1 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_S_Iberia_2 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_S_Iberia_3 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_mauritanicus__7 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_mauritanicus_1 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_mauritanicus_2 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_mauritanicus_3 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_mauritanicus_4 TAAAGTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_mauritanicus_5 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_mauritanicus__6 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_Cadiz_1 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGAGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_Cadiz_2 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGAGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_Cadiz_3 TAAATTTTGAATTTGATTTTTAAGTGAAAAAGCTTAAATGTTTTTGAGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_simplex_3 TAAATTTTGAATTTAATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAACAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_simplex_2 TAAATTTTGAATTTAATTTTTAAGTGAAAAAGCTTAAATGTTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATAATGATTAATAAAAAGTTTAGA Triops_mauritanicus_simplex_1 TAAATTTTGAATTTAATTTTTAAGTGAAAAAGCTTAAATATTTTTGGGGGACGATAAGACCCTATGGATCTTTATAATAATGATTAATAAAAAGTTTAGA Triops_longicaudatus_AY639934_ T-GTGACGGCTTACTGTTTTAAATTATTGGGTTGGGGCGACCGGAAGAAAAAAATATCTCTTCTTTAATA--ATATAA-TTTTTTTAGAAATAAAA-TGA Triops_granarius_AY115612_ TTGTAACAGCTTATTATTTTGAATTATTGGGTTGGGGCGACCAGGAGAAAAAAGTATCTCTTCTTAAATA--AAATAT-TATTAGTAGAAATAAAT-TGA Lepidurus_apus_apus__AY159584 GAGTTACGGCTTATTATAAATAAATATTGTGTTGGGGCGACTGAAAGAAATAAATATCTCTTTTT-AATAATAAATATAATTATATAGAAACATAA-TGA Lepidurus_apus_lubbocki_AY159583 -AGTTACGGCTTATGATTAATAAATATTGTGTTGGGGCGACTGAAAGAAATAATGATCTCTTTTT-AATAATAAATATAATTTTATAGAAATATAA-TGA Lepidurus_arcticus_AY159585_ GAGTTACGGCTTATTATAAATAAATATTGTGTTGGGGCGACTGAAAGAAATAAATATCTCTTTTT-AATAATAAATATAACTTTATAGAAGTATAA-TGA Lepidurus_lemmoni_AY115614_ CAGTTACGGCTTATTGTAAATAAATATTGTGTTGGGGCGACTGAAAGAAATAATTATCTCTTTTT-AATAATAAATAGAATTCCGTAGAAATATAA-TGA Triops_cancriformis_cancriformis_1 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAGAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAATTAAAAATGA Triops_cancriformis_cancriformis_2 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGGAGAAAAGAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAATTAAAAATGA Triops_cancriformis_cancriformis_8 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAGAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAATTAAAAATGA Triops_cancriformis_cancriformis_5 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAGAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAATTAAAAATGA Triops_cancriformis_cancriformis_3 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAGAATATCTCTTCTTAAAAA-TAAATAT-TATTCATAGAATTAAAAATGA Triops_cancriformis_cancriformis_4 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAGAATATCTCTTCTTAAAAA-TAAATAT-TATTCATAGAATTAAAAATGA Triops_cancriformis_cancriformis_6 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAGAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAATTAAAAATGA Triops_cancriformis_cancriformis_7 -AGTTACAGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAATTAAAAATGA Triops_mauritanicus_Gitanilla -AGTTACGGTCTTTTATTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGGAATAAAAATGA Triops_mauritanicus_Portugal -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTAGAAGAAAAAAATATCTCTTCTTAAAAAATAGATAT-TATTTATAGGAATAAAAATGA Triops_mauritanicus_S_Iberia_1 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTGTAGAAATAAAAATGA Triops_mauritanicus_S_Iberia_2 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATATGTAGAAATAAAAATGA Triops_mauritanicus_S_Iberia_3 -AGTTATGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTGTAGAAATAAAAATGA Triops_mauritanicus_mauritanicus__7 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGGAATAAAAATGA Triops_mauritanicus_mauritanicus_1 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGGAATAAAAATGA Triops_mauritanicus_mauritanicus_2 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATCTATAGGAATAAAAATGA Triops_mauritanicus_mauritanicus_3 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATCTATAGGAATAAAAATGA Triops_mauritanicus_mauritanicus_4 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGGAATAAAAATGA Triops_mauritanicus_mauritanicus_5 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTAGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGGAATAAAAATGA Triops_mauritanicus_mauritanicus__6 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCCTAAAAA-TAAATAT-TATTTATAGGAATAAAAATGA Triops_mauritanicus_Cadiz_1 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAAATAAAA-TGA Triops_mauritanicus_Cadiz_2 -AGTTACGGCTTTTTACTTTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-TATTTATAGAAATAAAA-TGA Triops_mauritanicus_Cadiz_3 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAA-TATCTCTTCTTAAAAA-TAAATAC-TATTTATAGAAATAAAA-TGA Triops_mauritanicus_simplex_3 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-AATTTATAGGAATAAAAATGA Triops_mauritanicus_simplex_2 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAACATCTCTTCTTAAAAA-TAAATAT-AATTTATAGGAATAAAAATGA Triops_mauritanicus_simplex_1 -AGTTACGGCTTTTTACTCTAAGTTATTGGGTTGGGGCGACTGGAAGAAAAAAATATCTCTTCTTAAAAA-TAAATAT-AATTTATAGGAATAAAAATGA Triops_longicaudatus_AY639934_ CCCTGAATTTTGGTTTAAAAGACTAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATAAAAAGGTTTGCGACCTCGATGTTGG Triops_granarius_AY115612_ CCCTGAATTTTGGTTTAAAAGACTAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAGGGTTTGCGACCTCGATGTTGG Lepidurus_apus_apus__AY159584 CCCTTAATTTTGGTTTATAAGACTAAGTTACCCTAGGGATAACAGCGTAATTTTTTCAGAGAGTTCTTATCGATGAGAAGGTTTGCGACCTCGATGTTGG Lepidurus_apus_lubbocki_AY159583 CCCTTAATTTTGGTTTATAAGACTAAGTTACCCTAGGGATAACAGCGTAATTTTTTCAGAGAGTTCTTATCGATGAAAAAGTTTGCGACCTCGATGTTGG Lepidurus_arcticus_AY159585_ CCCTTAATTTTGGTTTATAAGACTAAGTTACCCTAGGGATAACAGCGTAATTTTTTCAGAGAGTTCTTATCGATGAAAAAGTTTGCGACCTCGATGTTGG Lepidurus_lemmoni_AY115614_ CCCTTAATTTTGGTTTATAAGACTAAGTTACCCTAGGGATAACAGCGTAATTTTTTCAGAGAGTTCTTATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_1 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_2 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_8 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_5 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCTTATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_3 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_4 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_6 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_cancriformis_cancriformis_7 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_Gitanilla TCCTAAATTTTGGTTTAATAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_Portugal CCCTAAATTTTGGTTTACTAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_S_Iberia_1 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_S_Iberia_2 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_S_Iberia_3 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_mauritanicus__7 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGGAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_mauritanicus_1 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGGAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_mauritanicus_2 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGGAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_mauritanicus_3 CCCTAAATTTTGGTTTAGCAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGGAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_mauritanicus_4 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGGAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_mauritanicus_5 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGGAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_mauritanicus__6 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGGAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_Cadiz_1 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_Cadiz_2 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_Cadiz_3 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_simplex_3 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_simplex_2 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_mauritanicus_simplex_1 CCCTAAATTTTGGTTTAACAGATCAAGTTACCCTAGGGATAACAGCGTAATCTTTTTGGAGAGTTCATATCGATGAAAAGGTTTGCGACCTCGATGTTGG Triops_longicaudatus_AY639934_ ATTAAGAGATCCTTGCGGCGCAGCCGTTGTAA Triops_granarius_AY115612_ ATTAAGAGACCCTTACGGCGCAGCCGTTGTAA Lepidurus_apus_apus__AY159584 ATTAAGATATCCTTATGGCGCAGCTGT-ATAA Lepidurus_apus_lubbocki_AY159583 ATTAAGATATCCTTACGGCGCAGCTGTTGTAA Lepidurus_arcticus_AY159585_ ATTAAGATATCCTTATGGCGCAGCTGTTATAA Lepidurus_lemmoni_AY115614_ ATTAAGATATCCTTATGGCGCAGCTGTTATAA Triops_cancriformis_cancriformis_1 ATTAAGAGATCCTTGCGGCGCAGCAGTTGCGG Triops_cancriformis_cancriformis_2 ATTAAGAGATCCTTGCGGCGCAGCANTTGCGG Triops_cancriformis_cancriformis_8 ATTAAGAGATCCTTGCGGCGCAGCAGTTGCGG Triops_cancriformis_cancriformis_5 ATTAAGAGATCCTTGCGGCGCAGCAGTTGCGG Triops_cancriformis_cancriformis_3 ATTAAGAGATCCTTGCGGCGCAGCAGTTGCGG Triops_cancriformis_cancriformis_4 ATTAAGAGATCCTTGCGGCGCAGCAGTTGCGG Triops_cancriformis_cancriformis_6 ATTAAGAGATCCTTGCGGCGCAGCAGTTGCGG Triops_cancriformis_cancriformis_7 ATTAAGAGATCCTTGCGGCGCAGCAGTTGCGG Triops_mauritanicus_Gitanilla ATTAAGAGATCCTTACGGCGCAGCAGTTGAAA Triops_mauritanicus_Portugal ATTAAGAGATCCTTGCGGCGCAGCAGTTGAAA Triops_mauritanicus_S_Iberia_1 ATTAAGAGATCCTTGCGGCGCAGCAGTTGAAA Triops_mauritanicus_S_Iberia_2 ATTAAGAGATCCTTGCGGCGCAGCAGTTGAAA Triops_mauritanicus_S_Iberia_3 ATTAAGAGATCCTTGCGGCGCAGCAGTTGAAA Triops_mauritanicus_mauritanicus__7 ATTAAGAGATCCTTGCGGCGTAGCAGTTGAAA Triops_mauritanicus_mauritanicus_1 ATTAAGAGATCCTTGCGGCGTAGCAGTTGAGA Triops_mauritanicus_mauritanicus_2 ATTAAGAGATCCTTGCGGCGTAGCAGTTGAGA Triops_mauritanicus_mauritanicus_3 ATTAAGAGATCCTTGCGGCGTAGCAGTTGAGA Triops_mauritanicus_mauritanicus_4 ATTAAGAGATCCTTACGGCGTAGCAGTTGAAA Triops_mauritanicus_mauritanicus_5 ATTAAGAGATCCTTGCGGCGTAGCAGTTGAAA Triops_mauritanicus_mauritanicus__6 ATTAAGAGATCCTTGCGGCGTAGCAGTTGAAA Triops_mauritanicus_Cadiz_1 ATTAAGAGATCCTTGCGGCGCAGTAGTTGAAA Triops_mauritanicus_Cadiz_2 ATTAAGAGATCCTTGCGGCGCAGTAGTTGAAA Triops_mauritanicus_Cadiz_3 ATTAAGAGATCCTTGCGGCGCAGTAGTTGAAA Triops_mauritanicus_simplex_3 ATTAAGAGATCCTTGCGGCGCAGCAGTTGAAA Triops_mauritanicus_simplex_2 ATTAAGAGATCCTTGCGGCGCAGCAGTTGAAA Triops_mauritanicus_simplex_1 ATTAAGAGATCCTTGCGGCGCAGCAGTTGAAA ; END; BEGIN TREES; Title ML_tree_16S; LINK Taxa = 'Triops_haplotypes'; TRANSLATE 1 Triops_longicaudatus_AY639934_, 2 Triops_granarius_AY115612_, 3 Lepidurus_apus_apus__AY159584, 4 Lepidurus_apus_lubbocki_AY159583, 5 Lepidurus_arcticus_AY159585_, 6 Lepidurus_lemmoni_AY115614_, 7 Triops_cancriformis_cancriformis_1, 8 Triops_cancriformis_cancriformis_2, 9 Triops_cancriformis_cancriformis_8, 10 Triops_cancriformis_cancriformis_5, 11 Triops_cancriformis_cancriformis_3, 12 Triops_cancriformis_cancriformis_4, 13 Triops_cancriformis_cancriformis_6, 14 Triops_cancriformis_cancriformis_7, 15 Triops_mauritanicus_Gitanilla, 16 Triops_mauritanicus_Portugal, 17 Triops_mauritanicus_S_Iberia_1, 18 Triops_mauritanicus_S_Iberia_2, 19 Triops_mauritanicus_S_Iberia_3, 20 Triops_mauritanicus_mauritanicus__7, 21 Triops_mauritanicus_mauritanicus_1, 22 Triops_mauritanicus_mauritanicus_2, 23 Triops_mauritanicus_mauritanicus_3, 24 Triops_mauritanicus_mauritanicus_4, 25 Triops_mauritanicus_mauritanicus_5, 26 Triops_mauritanicus_mauritanicus__6, 27 Triops_mauritanicus_Cadiz_1, 28 Triops_mauritanicus_Cadiz_2, 29 Triops_mauritanicus_Cadiz_3, 30 Triops_mauritanicus_simplex_3, 31 Triops_mauritanicus_simplex_2, 32 Triops_mauritanicus_simplex_1; TREE 16S_ML_PAUP_1_RR = (((1:0.050607,2:0.040726):0.003859,((((7:0.0,8:0.002454,9:0.002462,10:0.002478,(11:0.0,12:0.002438):0.002444,13:0.0):0.004987,14:0.0):0.021481,((15:0.023264,16:0.011593):0.001357,(20:0.0,(21:0.002517,(22:0.0,23:0.002407):0.002415):0.002499,24:0.00501,25:0.002469,26:0.002453):0.004965,(30:0.0,(31:0.002522,32:0.002578):0.002502):0.005003):0.002487,(17:0.0,18:0.002463,19:0.002453):0.002439):0.004189,(27:0.0,28:0.002531,29:0.002532):0.00345):0.086324):0.0882405,((3:0.012977,(5:0.015752,6:0.024725):0.008074):0.036749,4:0.023813):0.0882405); END; BEGIN TREES; Title MP_strict_consensus_tree_16S; LINK Taxa = 'Triops_haplotypes'; TRANSLATE 1 Triops_longicaudatus_AY639934_, 2 Triops_granarius_AY115612_, 3 Lepidurus_apus_apus__AY159584, 4 Lepidurus_apus_lubbocki_AY159583, 5 Lepidurus_arcticus_AY159585_, 6 Lepidurus_lemmoni_AY115614_, 7 Triops_cancriformis_cancriformis_1, 8 Triops_cancriformis_cancriformis_2, 9 Triops_cancriformis_cancriformis_8, 10 Triops_cancriformis_cancriformis_5, 11 Triops_cancriformis_cancriformis_3, 12 Triops_cancriformis_cancriformis_4, 13 Triops_cancriformis_cancriformis_6, 14 Triops_cancriformis_cancriformis_7, 15 Triops_mauritanicus_Gitanilla, 16 Triops_mauritanicus_Portugal, 17 Triops_mauritanicus_S_Iberia_1, 18 Triops_mauritanicus_S_Iberia_2, 19 Triops_mauritanicus_S_Iberia_3, 20 Triops_mauritanicus_mauritanicus__7, 21 Triops_mauritanicus_mauritanicus_1, 22 Triops_mauritanicus_mauritanicus_2, 23 Triops_mauritanicus_mauritanicus_3, 24 Triops_mauritanicus_mauritanicus_4, 25 Triops_mauritanicus_mauritanicus_5, 26 Triops_mauritanicus_mauritanicus__6, 27 Triops_mauritanicus_Cadiz_1, 28 Triops_mauritanicus_Cadiz_2, 29 Triops_mauritanicus_Cadiz_3, 30 Triops_mauritanicus_simplex_3, 31 Triops_mauritanicus_simplex_2, 32 Triops_mauritanicus_simplex_1; TREE 16S_MP_Strict = ((((3,5,6),4),(1,2)),(((7,8,9,10,(11,12),13),14),15,16,(17,18,19),(20,(21,(22,23)),24,25,26),27,28,29,(30,31,32))); TREE 16S_MP_MajRule = ((((3,5,6),4),(1,2)),(((((7,8,9,10,(11,12),13),14),(16,(20,(21,(22,23)),24,25,26),(30,(31,32))),(17,18,19)),(27,28,29)),15)); END; BEGIN ASSUMPTIONS; options deftype = unord; TYPESET * UNTITLED = unord: 1 - 432; Lset Base = ( 0.3384 0.1048 0.1906 ) Nst = 2 TRatio = 2.6656 Rates = gamma Shape = 0.5229 Pinvar = 0.5263; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 432; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 432; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6422785022538034094; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8001254528245031445; checksumv 0 2 3804175889 null; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 919 628; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #8001254528245031445 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; 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; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; 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.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; 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;