#NEXUS [nuclear ribosomal ITS/5.8S sequence data from Lavin et al. (2003) study of Robinieae and aligned with the Mac program Se-Al and exported in Nexus format - see software at http://evolve.zoo.ox.ac.uk/software.html?id=seal] Begin DATA; [See Data Block beginning on page 18 of Cmd_ref_v2.pdf. Useful PAUP documents include this Command Reference Document, second draft, as well as the PAUP 3.1 Manual (Paup_Doc_3.1.pdf), which can be found at http://paup.csit.fsu.edu/downl.html] Dimensions ntax=45 nchar=695; Format datatype=dna gap=- missing=?; Matrix [ 1 11 21 31 41 51 61 71 81 91 101 111 121 131 141 151 161 171 181 191 201 211 221 231 241 251 261 271 281 291 301 311 321 331 341 351 361 371 381 391 401 411 421 431 441 451 461 471 481 491 501 511 521 531 541 551 561 571 581 591 601 611 621 631 641 651 661 671 681 691 ] [ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ] Robinia_hispida_010688 TCATTGTCGATGCCCCTA-ACAAGCAACCGACCCGTGAATTCGT-TTAA---CTACTTAGGG-TTGGCTCGGGGTGCTGAGCACC-TCGACCTCCCTTGGG-TTAGGGGG-GAGGTCACGTC---GTG--CCCTCTCCTCTTAGCCGA---AACACAAA-CCCC-GGCGCGGAATGCGTCAAGGAATCATAAAATCGTTTCACGTGCTCTCGTCCACCT--GGGGGCTTTTGCTCGTACGGG-TGGCGTTGCAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCGTTAGGCTGAGGGCACGCCTGCCTGGGTGTCACACATCGTTGCCCC--TATGCCAATCGCCTCACTTT--GTA--GGTA-TTTGCTTGGGG-TGAATGTTGGCCTCCCGTGAGCTCTGTCTCACGGTTGGTTGAAAA-TCGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGA---TGCTC-GAGA-CCAATCATGGG--TAACTCC-ACC--AGAATTGGGCTCGGTGACCCACA--TGCGTCCCTTGGATGCTCC-CTAAGGAGACCTCAGGTCAGGCGG Robinia_viscosa_14351 TCATTGTCGATGCCCCTA-ACAAGCAACCGACCCGTGAATTTGT-TTAA---CTACTTAGGG-TTGGCTCGGGGTGCTTAGCACC-TCGACCTCCCTTGGG-TTA-GGGG-GAGGTCACGTT---GTG--CCCTCTCCTCTTAGCCGA---AACACAAA-CCCC-GGCGCGGAATGCGTCAAGGAATCATAAATC-GTTTCACGTGCTCTCGTCCACCT--GGGGGCTTTTGCTCGTACGGG-TGGCGTTGCAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCGTTAGGCTGAGGGCACGCCTGCCTGGGTGTCACACATCGTTGCCCC--AATGCCAATCGCCTCACTTT--GTA--GGTA-TTTGCTTGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCACGGTTGGTTGAAAA-TCGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGATGATGCTC-GAGA-CCAATCATGGG--TAACTCC-ACC--AGAATTGGGCTCGGTGACCCACA--TGCGTCCCTTGGATGCTCC-CTAAGGAGACCTCAGGTCAGGCGG Robinia_pseudoacacia_220488 TCATTGTCGATGCCCCTA-ACAAGCAACCGACCCGTGAATTTGT-TTGA---CTACTTAGGG-TTGGCTCGGGGTGCTTAGCACC-TCGACCTCCCTTGGG-TTA-GGGG-GAGGTCACGTT---GTG--CCCTCTCCTCTTAGCCGA---AACACAAA-CCCC-GGCGCGGAATGCGTCAAGGAATCATAAATC-GTTTCACGTGCTCTCGTCCACCT--GGGGGCTTTTGCTCGTACGGG-TGGCGTTGCAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCGTTAGGCCGAGGGCACGCCTGCCTGGGTGTCACACATCGTTGCCCC--AATGCCAATCGCCTCACTTT--GTA--GGTA-TTTGCTTGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCACGGTTGGTTGAAAA-TCGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGATGATGCTC-GAGA-CCAATCATGGG--TAACTCC-ACC--AGAATTGGGCTCGGTGACCCACA--TGCGTCCCTTGGATGCTCC-CTAAGGAGACCTCAGGTCAGGCGG Robinia_neomexicana_190789 TCATTGTCGATGCCCCAA-ACAAGCAACCGACCCGTGAATTTGT-TCAA---CTACTTAGGG-TTGGCTCGGGGTGCTTAGCACC-TCGACCTCCCTTGGG-TTAGGGGG-GAGGTCACGTT---GTG--CCCTCTCCTCTTAGCCGA---AACACAAA-CCCC-GGCGCGGAATGCGTCAAGGAATCAAAATTT-GTTTCACGTGCTCACGTCCACGT--GGGGGCTTTTGCTCGTACGGG------TTGCAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGCCTGCCTGGGTGTCACACATTGTTGCCCC--AATGCCAATCGCCTCTCTTT--GTA--GGTA-TTTGCTTGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCACGGTTGGTTGAAAA-TCGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGA---CGCTC-GAGA-CCAATCATGGG--TAACTCC-ACC--AGAATTGGGCTCGGTGACCCACA--TGCGTCCCTTGGATGCTCC-CTAAGGAGACCTCAGGTCAGGCGG Poissonia_hypoleuca_231089 TCATTGTCAATG-CCCG--ACAAGCAATCGACCCGTGAACTTGT-TTAA---CTACTTGGGG-TTGGCTCGGGGTGCTTTGCTCC-TCGACCTCCCTTTGG-TTAGGGGG-GAGGTGCTGC----GTG--CCCTCTCCTCTTAGCCGT---AAAACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTT-TTTTCACGTGGTGGCGTCCACCTG------------------CGTGGTGGCGTTGCAGC-ACGTTAAGTACAGTACAATGACTCTCGGCAACGGATATCTCGGTTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAGGCCATTAGGTCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--GATGCCAATCGCCTCACTTT--GTG--GGAA-TTTGGTCGGGG-TGAATGTTGGCCTCCCGTGAGCTATGTCTCGCGGTTGGTTGAAAA-TTGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGCGA---TGCTC-GAGA-CCAATCATGAG--TAACTCC-ACC--AGAATTGCTCTCGGCAACCCACT--TGCATCC-TTGGATGCTCA-TCAAGGGGACCTCAGGTCAGGCGG Poissonia_orbicularis_923 TCATTGTCAATG-CCTG--ACAAGCAATCGACCCGTGAACTTGT-TAAA---CTACTTGGGG-TTGGCTCGGGGTGCTTTGCTCC-TCGACCTCCCTTTGG-TTAGGGGGGGAGGTGCTGC----GTG--CCCTCTCCTTTTAGCCGT---AAAACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTT-GTTTCACGTGCTCGCGTCCACCTG------------------CGTGGTGGCGTTGCAGC-ACGTTAAGTACAA-----TGACTCTCGGCAACGGATATCTCGGTTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAGGCCATTAGGTCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--GATGCCAATCGTCTCACTTT--GTG--GGAA-TTTGCTCGGGG-TGAATGTTGGCCTCCCGTGAGCTATGTCTGGCGGTTGGTTGAAAA-TCGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGCGA---TGCTC-GAGA-CCAATCATGAG--TAACTCC-ACC--AGAATTGCTCTCTGTAACCCACT--TGCATCC-TTGGATGCTCA-TCAAGGGGACCTCAGGTCAGGCGG Poissonia_heterantha_5785 TCATTGTCAATG-CCTG--ACAAGCAATCGACCCGTGAACATGTTTTTA---CTACTTGGGG-TTGGCTCGGGGTGCTGCGTGCCCTCGACCTCCCTTGGG-CTAGGGGG-GAGGTGCTGC----GTG--CCCTTTCCTCTAAGCCAT---AACACAAA-CCCC-GGCGCGGAATGCGTCAAGGAATCATAATTT-GTTTCTCGTGCTCGCGTCCACCTG------------------TGGG-TGGCGTTGCAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACACTGTTGCCCC--GATGCAAATCGCCTCACTTC--GTG--GGTA-TTTGCTCGGGG-TGAATGTTGGCCTCCCGTGAGCTATGTCTCACGGTTGGTTGAAAA-TGGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGCGA---TGCTCGAGGAACCAATCATGGG--TAACTCC-ATC--GGAATTGTGCTCGGCAACCCACA--TGCATCC-TCGGATGCTCC-TCAAGGGGACCTCAGGTCAGGCGG Poissonia_weberbaueri_918 TCATTGTCAATG-CTTG--ACAAGCAATCGACCCGTGAACATGTTTTTA---CTTCTTGGGG-TAGGCTCGGGGTGCTGCGTGCCCTCGACCTCCCTTGGG-TTAGGGGG-GAGGTGCTGT----GTG--CCCTCTCCTCTAAGCCGT---AACACAAA-CCCC-GGCGCGGAATGCGTCAAGGAATCATAATTC-ATTTCACGTGCTCGTGTTCACCTG------------------TGGGGTGGCGTTGCAGC-ATGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGTATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTACGGT?AGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--GATGCCAATCGCCTCACTTT--GTG--GGTA-TTTGCTCGGGG-TGAATGTTGGCCTCCCATGAGCTATGCCTCATGGTTGGTTGAAAA-TTGAGTGCATGGTGTTGGGTGTACCATGATGGATGGTGG-TT-GAGCGA---TGCTCGAGGAACCAATCATGGG--TAACTCC-ACC--AAAATTGTGCTCGGTAACCCACA--TGAATCC-TCGGATGCTCC-TCAAGGGGACCTCAGGTCAGGCGG Sphinctospermum_constrictum_5120 TCATTGTCAATGCCTC---AAAAGCAATCGACCCGTGGACCCGTCCCTTCGGTTAATCGGGG-CTGGCTCGGGGTGCTTAGCTCC-TCGACCACCCCTGTG-CTAGGGGGTGTGGGTCACCT--CGTGGCCCCCATCCTCTCAGCCTCG--AACAAAAAACCCC-GGCGCGGAAAGCGTCAAGGAATCGAAATTC-TTTACACGTGCTCGCGTCTACCCG--GGGGCGTT-GCCCGCACGGG-TGGCGTTGCAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCTGAGGGCACGCCTGCCTGGGTGTCACACGCTGTTGCCCC--GAAGCCAATCGCCTCACCGCGCGTG--GGCA-TTTGCCAGGGG-TGAATGTTGGCCTCCCGTGAGCCTCGTCTCGCGGTTGGTTGAAAC-TCGAGTGCATGGTGTTGGGTG-GCCATGATGGATGGTGG-CT-GAGCGA---TGCTC-GAGA-CCAATCATGTG--CGACCCC-TCC--GTGATCGCGCTCGGAGACCCACA--TGCATCC-CAGGATGCTCC-TAGATGAGACCTCAGGTCAGGCGG Genistidium_dumosum_210890 TCATTGTCG------CTA-AATCGGAATCGACTCGCGAACTTGTTTTTACTACTATATGGGG-CAGGCTCGGGGCGCTTCGGCACCTCGACCTCCCTTGGG-CAAGGGGG-GTGGTCATGC----GTG-CCCTCCT-CTCTTAGCCTT---AACAAAAA-CCCC-GGCGCGGAACGCGTCAAGGAATCATAATTA--TTTCACGTGCTCGCGTC-----------------GCCCGTATGGG-TGGCGTCGCAGCAACGTTACCTAAAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGCCTGCCTGGGTGTCACACACTGTTGCCCC--GACGCCAATCGCATCACT-TAGGTG--GGCA-TTTGCGCGGGG-CGAATGTTGGCCTCCCGCGAGCTCCGTCTCACGGTTGGTTGAAAA-CTGAGCGCGTGGTGTCGGGCGTACCATGATGGATGGAGG-CT-GAGCGA--ATGCTCGAAGA-CCAATCATGGG--TAACCCC-ACC--GGAATCGGGCTCGGAGACCCACACACGCATCC-TTGGATGGTCG-TGAATGAGACCTCAGGTCAGGCGG Peteria_scoparia_Lott TCATTGTCGATGTCCCTA-AAAAGCAACCGACTCGCGAACATGTTTTTA---CTACTTGGGG-TTGGCTTGGGGTGCTTTGCACC-TCGACCTCCCTTGGG-CAAGGGGG-GAGGTCATGTC---GTG--CCCTCTCCTCTTAGCCTT---AACACAAA-CCCCCGGCGCGGAACGCGTCAAGGAATCATAATTA--TTTCACGTGCTCAAGTCGACTT--GGGGGCA-TAGCCCGTACGGG-TGGTGTTGAAGC-ACGTAATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGTTGAGGGCACGCCTGCTTGGGTGTCACACATCGTTGCTCC--AACGCCAATCGCCTCACCATGTGTG--GGCA-TTTGCTTGGGG-TGAATGTTGGCCTCCCGTGAGCTTGGTCTCACGGTTGGTTGAAAA-TTGAGCACATGGTGTATGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGAAGA-CCAATCATGGG--TCACCCC-ACC--AGGATCTTGCTCAGCAACCCACA--TGCATCC-CTGGATGCTCG-TTAATGAGACCTCAGGTCAGGCGG Peteria_thompsoniae_7048_2 TCATTGTCGATGTCCCTA-AAAAGCAACCGACTCGCGAACATGTTTTTA---CTACTTGGGG-TTGGCTTGGGGTGCTTTGCACC-TCGACCTCCCTTGGG-CAAGGGGG-GAGGTCATGTT---GTG--CCCTCTCCTCTTAGCCTT---AACACAAA-CCCCCGGCGCGGAACGCGTCAAGGAATCATAATTA--TTTCACGTGCTCATGTCGACCT--GGGGGCG-TAGCCCGTACGGG-TGGCGTTGAAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGTTGAGGGCACGCCTGCCTGGGTGTCACACATCGTTGCTCC--AACGCCAATCGCCTCACCATGTGTG--GGCA-TTTGCTTGGGG-TGAATGTTGGCCTCCCGTGAGCTTGGTCTCACGGTTGGTTGAAAA-TTGAGCACATGGTGTATGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGAAGA-CCAATCATGGG--TCACCCC-ACC--AGAATCCTGCTCAGCAACCCACA--TGCATCC-TTGGATGCTCG-TTAATGAGACCTCAGGTCAGGCGG Peteria_glandulosa_1502 TCATTGTCGATGTCCCTA-AAAAGCAACCGACTCGTGAACATGTTTTTA---CTACTTGGGG-TTGGCTTGGGGTGCTTTGCACC-TCGACCTCCCTTGGG-CAAGGGGG-GAGGTCATGTC---GTG--CCCTCTCCTCTTAGCCTT---AACACAAA-CCCCCGGCGCGGAACGCGTCAAGGAATCATAATTA--TTTCACGTGCTCAAGTCGACCT--GGGGGCG-TAGCCCATACGGG-TGGCGTTGCAGC-ACGTTATGTACAAA----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATTAGGTTGAGGGCACGCCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATCGCCTCACCATGTGTG--GGCA-TTTGCTTGGGG-TGAATGTTGGCCTCCCGTGAGCTTGGTCTCACGGTTGGTTGAAAA-TTGAGCACATGGTGTATGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGAAGA-CCAATCATGGG--TCACCCCCACC--AGAATCCTGCTCAGCAACCCACA--TGCATCC-TTGGATGCTCG-TTAATGAGACCTCAGGTCAGGCGG Olneya_tesota_011288 TCATTGTCGACGCCCC---ACAAGCAACCGACCCGCGAATATGT-TTTA---CTACTTGGGG-TTGGCTCGGGGTGTTTAGCACC-TCGACCTCCCTTGGG-TTAGGGGG-GAGGTCACGTTAGCGTG-ACCCTCTCCCCTTGGCCAT---AACACAAA-CCCC-GGCGCGGAATGCGTCAAGGAATAATAATTC-ATTTCACGTGCCCGTGTCCGCCC--AGGGGTGAT-TCCCGTACGGG-TGGGGACGCGGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTATTTGAACGCAAGTTGCGCCCGAAACCACTAGGTCGAGGGCACGTCTGCCTGGGTGTCACGCATTGTTGCTCC--GATGCCAATCGCCTCACTTT--GTG--GGCA-TTCGCTCGGGG-TGAATGTTGGCCTCCCGCGAGCCTCGTCTCACGGTTGGTTGAAAA-TTGAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGCGA---TGCTC-GAGA-CCAATCATGGG--TAACCTC-ACC--GGAATCGCGCTCGGTAACCCACA--TGCATCC-TTGGATGCTCC-CTAAGGAGACCTCAGGTCAGGCGG Coursetia_elliptica_11558 TCATTGTCGATGACCCG-AAAAAAAAACAGACCCGTGGACATGTTTTTA---CTACTCGGGG-TTGGCTCGGGGTGCTTAGCACC-TTGACCTCCCTTTGG-CAA-GGGGTGAGGCCACATT---GTG--CCCTCTCCTCTAAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTA-TTTCCACGTGCTCGCGTTGACCCG-GGGGGCGTA-GCCTGCACGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGTGTCACACATTGTTTCCCC--AATGCCAATCGCCTCACTTT--GTG--GGTA-TTTGCTAGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAAATCGAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTTA--ATGCTCGGAGA-CCAATCATGGG--TAACCTC-ACT--AGAATTGTGCTTGACAACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_polyphylla_8224 TCATTGTCGATGACCCG-AAAAACCAACAGACCCGTGGACATGTTTTTA---CAACTCGGGG-TTGGCTCGGGGTGCTTAGCACC-TTGACCTCCCTTTGG-CAA-GGGGTGCGGCCACATT---GTG--CCCTCTCCTCTAAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTA-TTTCCACGTGCTCGCGTTGACCCG-GGGGGCGTA-GCCTGCACGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATCAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTTCCCC--AATGCCAATCGCCTCACTTT--GTG--GGTA-TTTGCTAGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAAATCGAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTTA--ATGCTCGGAGA-CCAATCATGGG--TAACCTC-ACT--AGAATTGTGCTTGACAACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_oaxacensis_615 TCATTGTCGATGACCCG-AAAAAACAATAGACCTGTGGACATGTTTTTA---CTACTCGGGG-TTGGCTCGGGGTGCTTAGCACC-TTGGCCTCCCTTTGG-CAA-GGGGTGAGGCCACATT---GTG--CCCTCTCCTCTAAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTA-TTTCCACGTGCTCGCGTTGACCCG-GGGGGCGTA-GCCTGCATGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTTCCCC--AATGCCAATTGCCTCACTTT--GTG--GGTA-TTTGCTAGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTTTCGCGGTTGGTTGAAAAATGAAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-ACAATCATGGG--TAACCTC-ACT--AGAATTGTGCTCGACAACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_chiapensis_8202 TCATTGTCGATGACCCG-AAAAACCAACAGACCCGTGGACATGTTTTTA---CAACTCGGGG-TTGGCTCGGGGTGCTTAGCACC-TTGACCTCCCTTTGG-CAA-GGGGTGCGGCCACATT---GTG--CCCTCTCCTCTAAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTA-TTTCCACGTGCTCGCGTTGACCCG-GGGGGCGTA-GCCTGCATGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATTAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATCAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTTCCCC--AATGCCAATCGCCTCACTTT--GTG--GGTA-TTTGCTAGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAAATCGAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTTA--ATGCTCGGAGA-CCAATCATGGG--TAACCTC-ACT--AGAATTGTGCTTGACAACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_madrensis_4626 ACATTGTCGATGACC-G-AAAAAATAATAGACCCGTGGACATGTTTTTA---CTACTCGGGG-TTGGCTCGGGGTGCTTAGCACC-TTGGCCTCCCTTTGG-CAA-GGGGTGAGGCCACATT---GTG--CCCTCTCCTCTAAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTA-TTTCCACGTGCTCACGTTGACCCGGGGGGCCGTA-GCCTGCATGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTTCCCC--AATGCCAATTGCCTCACTTT--GTG--GGTA-TTTGCTAGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAAATCAAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGGG--TAACCTC-ACT--AGAATTGTGCTCGACAACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_planipetiolata_5355 TCATTGTCGATGACCCG-AAAAAACAATAGACCCGTGGACATGTTTTTA---CTACTCGGGG-TTGGCTCGGGGTGCTTAGCACC-TTGGCCTCCCTTTGG-CAA-GGGGTGAGGCCACATT---GTG--CCCTCTCCTCTAAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCTTAATTA-TTTCCACGTGCTCGCGTTGACCCG-GGGGGCGTA-GCCTGCATGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACACTGTTTGCCC--AATGCCAATTGCCTCACTTT--GTG--GGTA-TTTGCTAGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAAATCAAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGGG--TAACCTC-ACT--AGAATTGTGCTCGACAACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_paniculata_5320 TCATTGTCGATGACCCG-AAAAAACAATAGACCCGTGGACATGTTTTTA---CTACTCGGGG-TTGGCTCGGGGTGCTTAGCACC-TTGGCCTCCCTTTGG-CAA-GGGGTGAGGCCACATT---GTG--CCCTCTCCTCTAAGCCTT---AACATAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATTA-TTTCCACGTGCTCGCGTTGACCCG-GGGGGCGTA-GCCTGCATGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTTCCCC--AATGCCAATTGCCTCACTTT--GTG--GGTA-TTTGCTAGGGG-TGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAAATCAAGCGCATGGTGTCCGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGGG--TAACCTC-ACT--AGAATTGTGCTCGACAACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_ferruginea_613 TCATTGTCGATGACCCG-AAAAAACAACAGACCCGCGGACTTGTATTTC---CTACTTGGGG-TTGGCTCGGGGTGCTCAGCACC-TCGACCAACCTAGGG-CAAAGGGGCGAGGCCACATC---GTG--CCCTCTCCTCTTAGCCTTCATAACACAAA-CCCC-GGCGCGAAAAGCGTCAAGGAATCATGATCA-TTTTCACGTGCTCGCGTCGACCCG-AGGGGCGTA-GCCCACGAGGG-TGGCGTCGTGAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCGCACATTGTTGCCCC--AACGCCAATCGCCTCACTTTT-GTG--GGCG-TTTTGCAGGGGGTGAATGTTGGCCTCCCGTGAGCTCTGTCTCGCGGTTGGTTGAAATATCGAGTGCACGGTGTCGGGCGTACCGTGATGCATGGTGGTTT-GAGTGA--ATGCTCGGAGA-CCAATCACGCG--TAACCCC-ACC--AGCGTTGTGCTCGGGGACCCACG--TGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_brachyrhachis_Lewis TCATTGTCGATGACCCG-AAAAAACAACAGACCCGCGGACGTGTTTTTA---CTACTTGGGG-CTGGCTCGGGGTGCTAAGCACC-TGGACCTCCCTTTGG-CAAGGGGGCGAGGGCACATT---GTG--CCCTCTCCTCTTAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATCA-TTTTCACGTGCTCGCGTCGACCTG--GGGGCGTA-GCCCGCACGGG-TGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATCGCCTCACTTGT-GTG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTGTGCCTCGCGGTTGGTTGAAAAATCGAGTGCATGGTGTCGGGCATACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGCG--TAACCTC-ACC--AGAGTCGTGCTCGGTGACCCACA--TGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_fruticosa_921 TCATTGTCGATGACCCG-AAAAAACAATAGACCCGCGGACGTGTTTTTA---CTACTTGGGG-CTGGCTCGGGGTGCTCAACACC-TCGACCTCCCTTGGG-CAAAGGGGCGAGGCCACATC---GTG--CCCTCTCCTCTTAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATCA-TTTTCACGTGCTCGCGTCGACCTG-GGGGGCCTA-GGCCGCACGGG-TGGCGTCGTAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATCGCCTCACTTTT-GTG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTGTGCCTCGCGGTTGGTTGAAAAATCGAGCACATGGTGTCGGGCGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGCG--TAACCTC-ACC--AGAGTCGTGCTCGGCGACCCACA--TGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_glandulosa_4671 TCATTGTCGATGACCCG-AAAAAACAACAGACCCGCGGACTTGTTTCTA---CTACTCGGGG-CTGGCTCGGGGTGCTCAGCGCC-TCGACCTCCCTTGGG-CAACGGGGCGAGGCCACATC---GTG--CCCTCTCCTCTCAGCCTC---AACACAAAACCCC-GGCGCGAAAAGCGTCAAGGAACCGTAATCA-TTTTCACGTGCTCGCGTCGACCCG-GGGGGCGCA-GCCCGCACGGG-CGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCGCACATTGTTGCCCCCCAACGCCAATCGCCTCACTTTT-GTG--GGCG-TTTGCTCGGGGGTGAATGTTGGCCTCCCGTGAGCTCTGCCTCGCGGTTGGTTGAAAA-TCGAGCGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGCG--TAACCTC-ACC--AGAGTCGCGCTCGGCGACCCACG--TGCATCC-TCGGATGCCCT-CCATGGAGACCTCAGGTCAGGCGG Coursetia_axillaris_271287 TCATTGTCGATGACCCG-AAAAAGCAACAGACCCGCGAACATGTTTTCA---CTACTCGGGG-TTGGCTCGGGGTGCCTGGCACC-TCGACCTCCCTTGGG-CAA-GGGGCGAGGCCACGTC---GTG--TCCTCTCCTCTTAGCCTTT--AACACAAA-CCCC-GGCGCGAAAAGCGTCAAGGAATCATAATTA--TCTCACGTGCTCGCGTCGACTCG-GGGGGCGTA-GCCCGTACGGG-TGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACACTGTTGCCCC--AACGCCAATCGCCTCACTCT--GTG-GGGCA-TTTGCCAGGGG-CGAATGTTGGCCTCCCGTGAGCTCCGCCTCGCGGTTGGTTGAAAAATCGAGCGCGCGGTGTCGGGCGTACCATGATGGACGGTGG-TT-GAGTGA--ATGCTCGAAGA-CCAATCATGGG--CGACCTC-ACC--AGAATCGGGCTCGGCAACCCATG--TGCATCC-TCGGATGCCCTCTCATGGAGACCTCAGGTCAGGCGG Coursetia_insomniifolia_5732a TCATTGTCGATGACCCA-AAAAAGCAACAGACCCGCGGACATGTTTTTA---CTACTTGGGG-TTGGCTCGGGGTGCCTGGCACC-TCGACCTCCCTTGGG-CAA-GGGGCGAGGCCACGTC---GTG--TCCTCTCCTCTTAGCCTTT--AACACAAA-CCCC-GGCGCGAAAAGCGTCAAGGAATCATAATTA--TCTCACGTGGTCGCGTCGACTCG-GGGGGCGTA-GCCCGTACGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACACTGTTGCCCC--AATGCCAATCGCCTCACTTT--GCGGGGGCA-TTTGGCAGGGG-TGAATGTTGGCCTCCCGTGAGCTCCGTCTCGCGGTTGGTTCAAAAATCGAGCGCGTGGTGTCGGTTGTACCATGATGGATGGTGG-TT-GAGTGA--ACGCTCGAAGA-CCAATCATGCG--CAACCTC-ACC--AGAATCGGGCTCGGGAACCCACG--TGCATCC-TCGGATGCTCTCTCATGGAGACCTCAGGTCAGGCGG Coursetia_pumila_5006 TCATTGTCGATGACCC--AAAAAACAACAGACCCGCGGACATGTTTATA---CTACTCGGGG-TTGGCTCGGGGCGCCCGACGCC-GCGACCTCCCCTGGG-CAAGGGGGCGAGGCCACATC---GTG--CCCTCTCCCCTCAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAACCATAATCA-TTTTCACGTGCTCGCGTCGACCCG--GGGGCGGA-GCCCGCACGGG-CGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACCTCAACCGCCTCGCTTTTTGCG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTTCGCCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGAGG-CCAATCATGCG--TAGCCTC-ACC--ATAGTCGAGCTCGGCGACCCGCG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_hidalgoana_100588 TCATTGTCGATGACCC--AAAAAACAACAGACCCGCGGACATGTTTCTA---CTACTCGGGG-TTGGCTCGGGGCGCTCGACGCC-GCGACCTCCCCTGGG-CAAGGGGGCGAGGCCACATC---GTG--CCCTCTCCCCTCAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAACCATAATCA-TTTTCACGTGCTCGCGTCGACCCG--GGGGCGGA-GCCCGCACGGG-CGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACCTCAACCGCCTTGCTTTTTGCG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTTCGCCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGAGG-CCAATCATGCG--TAGCCTC-ACC--ATAGTCGTGCTCGGCGACCCGCG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_glabella_4960 TCATTGTCGATGACCCG-AAAAAACAATAGACCCGCGGACATGTTTCTA---CTACTCGGGG--TGGCTCGGGGCGCCCGGCGCC-GTGACCTCCCCTGGG-CAAGGGGGCGAGGCCACATC---GTG--CCCTCTCCCCTTAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAACCATAATCA-TTTTCACGTGCTCGCGTCGACCCG--GGGGCGGA-GCCCGCACGGG-CGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACCTCAACCGCCTCGCTTTTTGCG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTCTGTCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGAGG-CCAATCATGCG--TAGCCTC-ACC--ATAGTCGTGCTCGGCGACCCGCG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_caribaea_trifoliolata_5189 TCATTGTCGATGACCCG-AAAAAACAACAGACCCGCGGACATGTTTCTA---CTACTTGGGG-TTGGCTTGGGGCGCTCGGCGCC-TCGACCTCCCCTGGG-CAAGGGGGCGAGGCCACATC---GTG--CCCTCTCCCCTCAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAACCATAATCA-TTTTCACGTGCTCGCGTCGACCGG---GGGCGGA-GCCCGCACGGG-CGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACCTCAACCGCCTCGCTTTTTGCG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTCCGTCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGAGG-CCAATCATGCG--TAGCCTC-ACC--ATAGTCGTGCTCGGCGACCCACG--GGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_caribaea_4603 TCATTGTCGATGACCCG-AAACAACAATAGACCCGCGGACATGTTTCTA---TTACTCGGGG-TTGGCTCGGGGTGCCCAGCGCC-TCGACCTCCCCTGGG-CAAGGGGGCGAGGCCACATT---GTG--CCCTCTCCCCTCAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAACCATAATCA-TTTTCACGTGCTCGCGTCGACTCG--GGGGCGGA-GCCCGCACGGG-CGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAACCGCCTCGCTTTTTGCG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTCCGTCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGAGG-CCAATCATGCG--TAGCCTC-ACC--ATAGTCGTGCTCGGCGACCCACG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_caribaea_ocholeuca_1063 TCATTGTCGATGACCCG-AAAAAACAACAGACCCGCGGACATGTTTTTA---CTACTCGGGG-CTGGCTCGGGGCGCTCGGCGCC-TCGACCTCCCCTGGG-CAAGGGGGCGAGGCCACATC---GTG--CCCTCTCCTCTCAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAAACACAATCA-TTTACACGTGCTCGCGTCGACCCG--GGGGCGGA-GCCCGCACGGG-CGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACTCCAACCGCCTCGCTTTT-GCG--GGCG-TTTGCCGGGGGGTGAATGTTGGCCTCCCGTGAGCTTCGTCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTAGGGCGTACCATGATGGATGGTGGTTTTGAGTGA--ATGCTCGGAGA-CCAATCGTGCG--TAGCCTC-ACCAAAGAGTCGTGCTCGGCGACCCACG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_andina_5732 TCATTGTCGATGACCCG-AAAAAACAACAGACCCGCGGACATGTTTCTA---CTACTCGGGG-TTGGCTCGGGGCGCCCAGCGCC-TCGACCTCCCCTGGG-CAAGGGGGCGAGGCCACATC---GTG--CCCTCTCCCCTCAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAACCATAATCA-TTTTCACGTGCTCGCGTTGACCCG--GGGGCGGA-GCCCGCACGGG-CGGCGTCGCAAC-ACGTTATGTATAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTACCCC--AACGCCAACGGCCCCGCTTTTTGTG--GGCG-TTTGCTAGGGGGTGAATGTTGGCCTCCCGTGGGCTACGTCTCGCGGTTGGTTGAAAACTCGAGTGCATGGTGTTGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGAGG-CCAATCATGCG--TAGCCTC-ACC--ATAGTCGTGCTCGGCGACCCACG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_vicioides_938 TCATTGTCGATGACCCG-AAAAAGCAACAGACCCGCGGACCAGTTTTTA---CTACTCGGGGGCTGGCTCGGGGTGCTCAGCACC-TCGACCTCCCTTGGG-CAA-GGGGCGAGGCCACACT---GTG--CCCCCTCCTCTTAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATCA-TTCTCACGTGCTCGCGTCGACCCG-GGGGGCGTA-GCCCGAACGGG-TGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACACTGTTGCCCC--AACGCCAATCGCCTCACTTTT-GTG--GGTG-CTTGCCAGGGGGCGAACGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAAATCGAGCGCGCGGTGTCGGGCGCACCATGATGGATGGTGGTT--GAGTGA--ATGCTCGGGGA-CCAATCATGGGTGTAACCTC-ACC--AGAGTCGTGCTCGGCGACCCACG--GGCATCC-TCGGATGCTCT-TCACGGAGACCTCAGGTCAGGCGG Coursetia_hassleri_5809 TCATTGTCGATGACCC--AAAAAACAACAGACCCGCGGACATGTTTCTA---CTACTCGGGG-TTGGCTCGGGGCGCCTAGCGCC-TCGACCTCCCCTGGG-CAG-GGGGCGAGGCCACATC---GGG--CCCTCTCCTCTCAGCCTG---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCACAATCA-TTTTCGCGTGCTCGCGTCGACCCG--GGGGCGGA-GCCCGCACGGG-TGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATCGCCTTGCTTTT-GCG--GGCG-TTTGCCAAGGGGTGAATGTTGGCCTCCCGTGAGCTCCGTCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGAGA-CCAATCATGCG--TAGCCTC-ACC--ATAGTCGCGCTCGGCGACCCACG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_hassleri_13478 TCATTGTCGATGACCCG-AAAAAACAACAGACCCGCGGACATGTTTCTA---CTACTCGGGG-TAGGCTCGGTGCGCTCTGCGCC-TCGACCTCCCTTGGG-CAAGGGGGCGGGGCCACATC---GTG--TCCTCTCCTCCAAGCCTT---AACACAAA-CCC--GGCGCGAAAAGCGTCAAGGAATCACAATCA-TTTTCGCGTGCTCGCGTGGACCCG--GGGGCGGA-GCCCGCACGGG-GGGCGTCGCAGC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AAAGCCAACCGCCTCGCTTTT-GCG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGCTCCGTCTCGCGGTTGGTTGAAAACTCGAGTGCATGGTGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGG--ATGCTCGGAGA-CCAATCATGCG--TAGCCTC-GCC--ATAGGAGCGCTCGGCGACCCACG--GGCATCC-TCGGATGCTCT-TCAAGGAGACCTCAGGTCAGGCGG Coursetia_dubia_926 TCATTGTCGATGACCCGAAAAAATAAATAGACCAGCGGACATGTTTCTA---CTACTTGGGG-TTGGCTCGGGGTGCTCAGCGCC-TCAACCTCCCCTTGGGCAAGGGGGCGAGGCCACATT---GTG--CCCTCTCCTCTCAGCCTT---AACAAAAA-CCCC-GGCGCGAAAAGCGTCAAGGAATCATAATCG-TTTTCACGTGCTCGCGTCGACCCTGGGGGGCACA-GCCCACACGGGGTGGCGTTGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATTGCCTCACTTTT-GTG--GGCA-TTTGTTAGGGGGTGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAACTGGAGTGCATGGTGTCGGGTGTACCATGATGGATGGTGG-TC-GAGTGA--ATGCTCGAAGG-CCAATCATGTG--TAACCTC-ACC--AGAGTAGTGCTCGGTGACCCACA--TGCATTC-TCGGATGCTTT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_grandiflora_929 TCATTGTCGATGACCCGAAAAAATAAATAGACCAGCGGACGTGTTTCTA------CTTGGGG-TTGGCTCGGGGTGCTCAGCGCC-TCAACCTCCCCTTGGGCAAGGGGGCGAGGCCACATT---GTG--CCCTCTCCTCTCAGCCTT---AACAAAAA-CCCC-GGCGCGAAAAGCGTCAAGGAATCATAATCG-TTTTCACGTGCTCGCGTCGACCCTGGGGGGCACA-GCCCACACGGGGTGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATTGCCTCACTTTT-GTG--GGCG-TTTGTTAGGGGGTGAATGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAACTCGAGTGCATGGTGTCGAGTGTACCATGATGGATGGTGG-TC-GAGTGA--ATGCTCGAAGG-CCAATCATGTG--TAACCTC-ACC--AGAGTAGTGCTCGGTGACCCACA--TGCATTC-TCGGATGCTTT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_gracilis_629 TCATTGTCGATGACCCGAGAAAATAA-CAGACCCGCGAACATGTTTCCA---CTACTCGGGG-TTGGCTCGGGGTGCTCAGCGCC-TCGACCTCCCTTTGG-CAAGTGGGCGAGGCCACATC---GTG--CCCTCTCCTCTTAGCCTT---AACAAAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATCA-TTTTCACGTGCTCGCGTCGACCC-GGGGGGCACA-GCCCACACGGG-TGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATTGCCTCACTTTT-GTG--GGCG-TTTGTCAGGGG-TGAACGTTGGCCTCCCGTGAGCTTTGTCTCGCGGTTGGTTGAAAACTCGAGCGCATGGTGTCCGGTGTGCCGTGATGGATGGTGG-TC-GAGTTA--ACGCTCGAAGG-CCAATCATGTG--TAACCTC-ACC--AGAGTCGTGCTCGGCGACCCACA--TGCATTC-TCGAATGCTCT-CCATGGAGACCTCAGGTCAGGCGG Coursetia_hintonii_1030 TCATTGTCGATGACTCG-AAAAAACAACAGACCCGCGGACGTGTTTTGA---CTACTTGGGG-TTGGCTCGGGGCGCTCAGCACC-TCGACCTCCCTTGGG-CAA-GGGGCGAGGCCACATC---GTG--CCCCCTCCCCTTAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAACCATAATCA-TTTTCACGTGCTCGTGTCGACCCGTGGGGGCATA-GCCTGCACGGG-TGGCATAGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAGCGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTCGCCCC--AACGCCAATCGCCTCACTTTT-GTG--GGAACTTTGCTAGGGGGTGAATGTTGGCCTCCCGTGAGCTCCGCCTCGCGGTTGGTTGAAAAATCGAGCGCATGGTGTTGGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGG-CCAATCATGGG--TAGCCAC-ACC--GGTGTTGTGCTCGACGACCCACA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_mollis_1031 TCATTGTCGATGACCCGAAAAAAACAAGAGACCCGCGGACATGTTTCTA---CCACTGGGGG-TTGGCTCGGGGCGCTCAGCTCC-TGGGCCTCCCCCGGG-CAAGGGGGCGAGGCCACACA---GTG--CCCTCTCCTCTTAGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCACNATCA-TTTTCGCGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGGG-TGGCGTCGCAAC-ACGTTATGTACAA-----TGACTTTCGGCANCGGATATCTCGGCTCTTGCATCGATGAAGAGCGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCTC--AA-GCCAACCGCCTTGCCTTT-GCG--GGCG-TTTGCCAGGGGGCGAATGTTGGCCTCCCGTGAGCTTCGTCTCGCGGTTGGTTGAAAACTCGAGTGCATGGCGTCGGGCGTACCATGATGGATGGTGGTTT-GAGTGA--ATGCTCGGGGA-CCAATCATGCG--TAGCCTC-GCC--ATAGTCGTGCTCGGCGACCCACG--CGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_maraniona_948 TCATTGTCGATGACCCG-AAAAAACAATAGACCCGTGGACGTTTTTTTA---CTACTTGGGG-CTGGCTCGGGGTGCTTAGGACC-TCGACCTCCCTTGGG-CAAGGGGGTGAGGCCACATC---GTG--CCCTCTCCTCTTAGCCTT---AACATAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATCA-TTTTCACGTGCTGGCGTCAACCTA-GGGGGCCTA-GCCCGCATGGG-TGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATTGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATCGCCTCACATTT-GTG--GGCG-TTTTCCAGGGG-TGAATGTTGGCCTCCCGTGAGCTGTGCCTTGCGGTTGGTTGAAAAATCGAGCGCATGGTGTC-GGTGTAGGATGATGGATGGTGG-TT-GAGTGA--ATGCTCTGAGA-CCAATCATGTG--TAACCCT-ACC--AGAGTCGTGCTCGTTGACCCATA--TGCATCC-TTGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_cajamarcana_1675 TCATTGTCGATGACCCG-AAAAAACAATAGACCCGTGGACGTGTTTTTA---CTACTTGGGG-CTGGCTCGGGGTGCTCAGCACC-TCGACCTCCCTTGGG-CAAGGGGGCGAGGCCACATT---GTG--CCCTCTCTTCTTAGCCTT---AACATAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATCA-TTTTCACGTGCTCGCGTCGACCTG-GGGGGCCTA-GCCCGCATGGG-TGGCGTCGCAAC-ACGTTATGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACATTGTTGCCCC--AACGCCAATCGCCTCACTTTT-GTG--GGCG-TTTGCCAGGGGGTGAATGTTGGCCTCCCGTGAGTTGTGCCTTGCGGTTGGTTGAAAAATCGAGTGCATGGTGTCGGGCGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGCG--TAACCTC-ACC--AAAGTCGTGCTCGGCGACCCACA--TGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG Coursetia_rostrata_930 TCATTGTCGATGACCCG-AAAAAGCGACAGACCCGCGAACTAGTTTTTA---CTACTCGGGG-CTGGCTCGGGGTGCTCAGCACC-TCGACCTCCCTTGGG-CAA-GGGGCGAGGCCACATT---GTG--CCCCCTCCTCTTGGCCTT---AACACAAA-CCCC-GGCGCGGAAAGCGTCAAGGAATCATAATCA-TTCTCACGTGCTCGCGTCGACCCG-GGGGGCGTA-GCCCGAACGGG-TGGCGTTGCAAC-ACGTTACGTACAA-----TGACTCTCGGCAACGGATATCTCGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGTCTGCCTGGGTGTCACACACTGTTGCCCC--AACGCCAATCGCCTCACTTTC-GTG--GGTG-TTTGCCAGGGGGCGAATGATGGCCTCCCGTGAGCTTTGTCTCGTGGTTGGTTGAAAAATCGAGCGCGTGGTGT-GGGTGTACCATGATGGATGGTGG-TT-GAGTGA--ATGCTCGGAGA-CCAATCATGCGTGTAACCTG-ACC--AGAGTCGTGCTCGACGACCCACG--TGCATCC-TCGGATGCTCT-TCATGGAGACCTCAGGTCAGGCGG ; end; [Text in square brackets is disregarded by PAUP. See page 67 in Paup_Doc_3.1.pdf.] [When different, the commands reported Cmd_ref_v2.pdf are correct compared to those in Paup_Doc_3.1.pdf.] begin paup; [PAUP blocks are discussed on page 81 of Paup_Doc_3.1.pdf; and page 30 of Cmd_ref_v2.pdf. These are the main blocks for placing command statements.] log file=cour_par_log.nex replace; [See page 82 of Cmd_ref_v2.pdf. Logging output is simply a great way to store the general output of an analysis. The log file name designated after file= can be any.] outgroup 1-8; [See page 96 in Paup_Doc_3.1.pdf and page 96 of Cmd_ref_v2.pdf.] set criterion=parsimony taxlabels=full torder=right maxtrees=5000 increase=no root=outgroup outroot=monophyl storebrlens=yes warnreset=no warntree=no warntsave=no warnroot=no warnredef=no autoclose=yes; [See page 114 of Cmd_ref_v2.pdf for the Set command, which is useful for defining general options.] [delete Coursetia_caribaea_trifoliolata_5189;] [Delete eliminates taxa; page 49 of Cmd_ref_v2.pdf and page 105 of Paup_Doc_3.1.pdf.] [exclude 1-3;] [Exclude eliminates characters, which in this case involves characters 1, 2, and 3; page 60 of Cmd_ref_v2.pdf and page 94 of Paup_Doc_3.1.pdf.] [Search options depend on size of data set. If you are analyzing less than 10 terminal taxa, go to the bottom of this file and see the batch file commands for running branch and bound] [If you are analyzing a data set with more than 10 terminals but less than 100, try the following:] hsearch start=stepwise hold=2 addseq=random nreps=20 [limitperrep=yes rearrlimit=5000 timelimit=5000] swap=tbr steepest=yes multrees=yes; [Descriptions of the hsearch or heuristic search options begin on page 71 of Cmd_ref_v2.pdf. The strategy is to find the global optima by avoiding getting stuck in local optima. See pages beginning on 35 and again on 107 in Paup_Doc_3.1.pdf for general parsimony search strategies. The limitperrep options (use either the rearrangment or time limit) are used if the data set is large and taking many hours/days per random addition replicate. If data analysis is very rapid with the heuristic search, consider using the branch and bound (bandb) search instead, as described on page 37 of Cmd_ref_v2.pdf 32 of Paup_Doc_3.1.pdf.] [If you are analyzing a data set with 100's of terminals, try these options:] [hsearch start=stepwise hold=2 addseq=simple limitperrep=no usenonmin=yes swap=tbr steepest=yes multrees=yes;] describetrees 1/ root=outgroup plot=phylogram apolist=no; [Describetrees provides one useful way for generating text output of the tree along with tree statistics to the log file. If apolist=yes, then apomorphic changes per branch are reported, which is very useful for inspecting character codings of morphological traits. See page 51 of Cmd_ref_v1.pdf. See also page 60 of Paup_Doc_3.1.pdf for discussion of tree statistics.] savetrees root=yes file=cour_par_tre.nex replace format=altnex brlens=yes; [See page 112 in Cmd_ref_v2.pdf for saving trees. I tend to use the altnex and brlens format because of the requirements of the r8s program. The file name for the tree description output can by any, but note that I then append additional trees to this same file - see below.] contree all/strict=yes semistrict=no majrule=no adam=no root=outgroup treefile=cour_par_tre.nex append=yes; [See page 44 in Cmd_ref_v2.pdf for generating consensus trees, and page 56 of Paup_Doc_3.1.pdf for a discussion of consensus trees. Majority rule should be used only when summarizing bootstrap or jackknife replicates. Adams consensus provides an excellent way to identify a problematic terminal taxon because it will be resolved as the basal branch of some particular large clade. Problematic taxa include those with too much missing data or of hybrid origin, etc.] bootstrap nreps=500 [should be nreps=10000] grpfreq=no conlevel=70 search=heuristic/ addseq=random nreps=1 swap=TBR steepest=no multrees=no; [See page 39 in Cmd_ref_v2.pdf for generating a majority rule consensus from bootstrap replicates. See page 62 in Paup_Doc_3.1.pdf for a discussion of the bootstrap analysis. Bootstrap provides one measure of clade support, which obviates concerns about finding the absolute most parsimonious trees because then emphasis is placed on only relationships that are well supported. One efficient way of doing bootstraps includes many replicates with minimal searching per replicate (e.g., only one random addition per bootstrap replicate combined with no mulpars are steepest descent). This biases bootstrap values low.] savetrees from=1 to=1 root=yes file=cour_par_tre.nex append=yes format=altnex savebootp=brlens; [See page 112 in Cmd_ref_v2.pdf for saving trees.] charpartition data=1:1-274, 2:275-445, 3:446-.; exclude uninf; hompart partition=data nreps=500 [should be 10000]; [See page 70 of Cmd_ref_v2.pdf.] log stop; [See page 82 of Cmd_ref_v2.pdf.] end; [Branch and bound search algorithm for analyzing small data sets, typically involving less than 10 terminal taxa.] [ begin paup; [If a data set is small enough, a branch and bound parimony search can be performed, which in contrast to the heuristic search is guaranteed to find the most parsimonious solution. This can be done as follows on the above data set.] log file=cour_bnb_log.nex replace; outgroup 5-8; set criterion=parsimony taxlabels=full torder=right maxtrees=5000 increase=no root=outgroup outroot=monophyl storebrlens=yes warnreset=no warntree=no warntsave=no warnroot=no warnredef=no autoclose=yes; delete 1-4 9-27 Coursetia_vicioides_938 Coursetia_maraniona_948 Coursetia_cajamarcana_1675 Coursetia_rostrata_930; [In order to reduce the size of the above data set and make it amenable to a branch and bound search, delete a subset of taxa, including Sphinctospermum_constrictum_5120 through Coursetia_insomniifolia_5732a.] exclude 1-7 280-440 680-.; [In order to reduce the size of the above data set and make it amenable to a branch and bound search, exclude a subset of characaters.] bandb multrees=yes; [Descriptions of the branch and bound search options begin on page 37 of Cmd_ref_v2.pdf.] describetrees 1/ root=outgroup plot=phylogram apolist=no; savetrees root=yes file=cour_bnb_tre.nex replace format=altnex brlens=yes; contree all/strict=yes semistrict=no majrule=no adam=no root=outgroup treefile=cour_bnb_tre.nex append=yes; bootstrap nreps=50 [should be nreps=10000] grpfreq=no conlevel=70 search=bandb/ multrees=no; savetrees from=1 to=1 root=yes file=cour_bnb_tre.nex append=yes format=altnex savebootp=brlens; log stop; end; ]