#NEXUS [written Thu Oct 25 12:45:42 BST 2012 by Mesquite version 2.72 (build 527) at Salvi-PC/192.168.6.233] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=26; TAXLABELS Pecten_jacobaeus_1 Pecten_jacobaeus_2 Pecten_maximus_1 Pecten_maximus_2 Pecten_keppelianus_1 Pecten_keppelianus_2a Pecten_keppelianus_2b Pecten_novaezelandiae Amusium_pleuronectes Aequipecten_opercularis_2 Aequipecten_opercularis_1 Flexopecten_glaber_1 Flexopecten_glaber_2 Flexopecten_flexuosus Argopecten_irradians_ Manupecten_pesfelis_1 Manupecten_pesfelis_2 Semipallium_fulvicostata Talochlamys_multistriata Talochlamys_pusio Mimachlamys_varia_1 Mimachlamys_varia_2 Azumapecten_farreri Mizuhopecten_yessoensis Mimachlamys_nobilis Spondylus_gaederopous ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=383; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Pecten_jacobaeus_1 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_jacobaeus_2 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGGGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_maximus_1 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_maximus_2 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--GGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_keppelianus_1 AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGGGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA------------------------AATTG--AATCAC--TT Pecten_keppelianus_2a AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGGGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA------------------------AATTG--AATCAC--TT Pecten_keppelianus_2b AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA------------------------AATTG--AATCAC--TT Pecten_novaezelandiae AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGCA-CGAGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------------------AT-G--AATCAC--TT Amusium_pleuronectes GAAACATCTATCGCAA--CGTTATGCACACATCAAGC------GTTGCGCCTTGGACCGTACTAACTCCGTGTCGATTGCGCGTTGT---------------CGTGGCA-CGCGGAGCGGTCCGAA-ATGTTGAC-GATCGGAGTAAATTTCACACA-------GACCGAGTAGTTCGGTGTTGAGATCGCCC--GCAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CATATCAA-GTGCGCTCG---------------ACTGTCTCGCGAATC---------------GAAGGGCCTTTTCAAGT-GAGACTCCGTGAAG------------------------------TCGTTTTTCAATCTT--TTTT-----TC Aequipecten_opercularis_2 AAAACATCTATCGCAA--CTGCATGCACATACA--GC------GTTGCGCCTTGGATCGTACAACTCCACGTACGCCGTATTTCGA----------------GACGGAAACGAGGAGCGATCCCAA-ATGCAA-----TCGTCCCATCTCATAAAAAGC---CTAACCGAGTAGTTCGGTGTTGAAATCGCCCGTTTAACGG-ACGA-CCGAGA--CGCAGCTCGAAT--ATTAATCAAGTGCGCTCG---------------ACTGTTCAAAAAACC-------------------TTTGTGTGGTG-TTATTT-TCATTGGCT-----------GATGAA-------------GACGTTAAAAAAAA-----ATCAAAACC Aequipecten_opercularis_1 AAAACATCTATCGCAA--CTGCATGCACATACA--GC------GTTGCGCCTTGGATCGTACAACTCCACGTACGCCGTATTTCGA----------------GACGGAAACGAGGAGCGATCCCAA-ATGCAA-----TCGTCCCATCTCATAAAAAGC---CTAACCGAGTAGTTCGGTGTTGAAATCGCCCGTTTAACGG-ACGA-CCGAGA--CGCAGCTCGAAT--ATTAATCAAGTGCGCTCG---------------ACTGTTCAAAAAACC-------------------TTTGTGTGGTG-TTATTT-TCATTGGCC-----------GATGAA-------------GACGTTAAAAAAAA-----ATCAAAACC Flexopecten_glaber_1 AAAACATCTATCGCAA--CTGCGTGC--ATACGAAGC------GTTGCGCCTTGGACCGTACATCTCCTCGTCCGCCGT--TTTGT----------------GACGGCA-CGGGGAGCGGTCCCAA-ATGCA------TGTTTCCATC--ATAAAAG-----CCAACCGAGTAGTTCGGTGTTGAAATCGCCC-TTGAAGGG-ACGA-CCGAGA--CGCAGCTCGAAT--AACAATCAAGTGCGCTCG---------------ACTGTTCCCGAA-----------------------------GGCG-TTTTTC-TGACAGGCG-----------ATGGAA-------------CACTTTGAA-----------TCAAAACC Flexopecten_glaber_2 AAAACATCTATCGCAA--CTGCGTGC--ATACGAAGC------GTTGCGCCTTGGACCGTACATCTCCTCGTCCGCCGT--TTTGT----------------GACGGCA-CGGGGAGCGGTCCCAA-ATGCA------TGTTTCCATC--ATAAAAG-----CCAACCGAGTAGTTCGGTGTTGAAATCGCCC-TTGAAGGG-ACGA-CCGAGA--CGCAGCTCGAAT--AACAATCAAGTGCGCTCG---------------ACTGTTCCCGAA-----------------------------GGCG-TTTTTC-TGACAGGCG-----------ATGGAA-------------CACTTTGAA-----------TCAAAACC Flexopecten_flexuosus AAAACATCTATCGCAA--CTGCGTGC--ATACGAAGC------GTTGCGCCTTGGACCGTATATCTCCTCGTCCGCCGT--TTTGT----------------GACGGCA-CGGGGAGCGGTCCCAA-ATGCA------TGTTTCCATC--ATAAAAG-----CCAACCGAGTAGTTCGGTGTTGAAATCGCCC-TTGAAGGG-ACGAACCGAGA--CGCAGCTCGAAT--AACAATCAAGTGCGCTCG---------------ACTGTTCCCGAA-----------------------------GGCG-TTTTTC-TGACAGGCG-----------ATGGAA-------------CACTTTGAA-----------TCAAAACC Argopecten_irradians_ AGAATATCTATCGCAA--CTGCATGCACAT--GAAGC------GTTGCGCCTTGGACCGTACATCTCCACGTTTGTTTGCTTGAGA----------------AACGATA-CGAGGAGCGGTCTCAA-ATACACA---GTCGCATCATCGTTCGCCAAA----AAAACCGAGTAGTTCGGTGTTGAAATCGTCCGTGAAACGGAACGA-CCGAGA--CGCAGCTCGAAT-GATCAATCAAGTGCGCTCG---------------ACTGTTCCCGATGAA-------------------CATGTG-GGCA-TCATGG-T-ATCGGCG-----------ATGAGA-------------CTGACAAAAAAAACTC--TATCAAAAAC Manupecten_pesfelis_1 AAAACATCTATCGCAAA-CTGCATGCACATCAG---C------TTTGCGCCTTGGACCGGTTTTTACTGCCGTATTTGTTTATTTA----------------TAAGCAAAGAGGCAGCGGTCTTAAGAAAAAAA---GTCAGAGTCTC-----CAA------AATATTGAACGACATGTACAGCCCAGTGC----GGAACAAAAC-A-C-GAGAGACGCAGCTCGATA-GA--GATAAAATGCGCTGTCGGGTGT---TCCAAACTGAAATACGGGCC-------------------AACACATGAAC---AAACTGAAATGGTTTTTTTTTGGTGGTGTAA-------------TTCTCTGTCCTTAAAC-ATTTCTCACT- Manupecten_pesfelis_2 AAAACATCTATCGCAAA-CTGCATGCACATCAG---C------TTTGCGCCTTGGACCGGTTTTTACTGCCGTATTTGTTTATTTA----------------TAAGCAAAGAGGCAGCGGTCTTAAGAAAAAAA---GTCAGAGTCTC-----CAA------AATATTGAACGACATGTACAGCCCAGTGC----GGAACAAAAC-A-C-GAGAGACGCAGCTCGATA-GA--GATAAAATGCGCTGTCGGGTGT---TCCAAACTGAAATACGGGCC-------------------AACACATGAAC---AAACTGAAATGGTTTTTTTTTGGTGGTGTAA-------------TTCTCTGTCCTTAAAC-ATTTCTCACT- Semipallium_fulvicostata AAAACATCTATCGCAAA-CTGCAGGCACGTCAG---C------TTTGCGCCTTGGACCGGTTT---CTGTCGCATTTGTC-GGTAG----------------TGACGAGAGCGGCAGCGGTCTTAAGAAAAAAA---GTCAGAGTCTC-----CAG------AACA--------CATGTTGTGCCCAGCGA----GAGACA-------------GACGCAGGTCGATT-T---GATTAAATGCGCTGTCTT---------TG-AC----ATACGGGGGCC-----------------AACAAATTAAC-TAAAAGTGAAAAAAGTT---------GGTGTAA-------------TTCTCTGGCACGAAACGAGTTCTTACTC Talochlamys_multistriata ATAACATCTATCGCAAA-CTGCATGTACAGCAG---C------GTTGCGCCTTGGGCCG---------TATAACTCTCGTGTGGTAA----------------------A-TGAGAGCGGTCTCAA-ATAACGA---ATCAGAGTCTC-----CGAGCG---AACGCAGTTTGAGACGAAATA--------------AATTCAGT-A-C-GAGAGACGCAGCTCGATT-TG-----TGAAATGCGCTCTCAC------ACATGTACTGTGATTTTCGTTGAGTTCGCCAATGA---ATCAAATGT----ATGAAAACTCGGTGTAATTCTCTGCTCGGCA-A-------------T---ATGATTGCCTT----TTCACAC-- Talochlamys_pusio ATAACATCTATCGCAAA-CTGCGTGTACAGCAG---C------GTTGCGCCTTGGGCCG---------TATAACTCTCGTGTGGTAA----------------------A-TGAGAGCGGTCTCAA-ATAACGA---ATCAGAGTCTC-----CGAGCG---AACGCAGTTTGAGACGAAATA--------------AATTCAGT-A-C-GAGAGACGCAGCTCGATT-TG-----TGAAATGCGCTCTCAT------ATATGTACTGTGATTT-CGTTGAGTTCGCCAATGA---ATCAAATGT----ATGAAAACTCGGTGTAATTCTCTGCTCGGCATA-------------T---ATAATTGCCTG----TTCACAC-- Mimachlamys_varia_1 ATAACATCTATCGCAAA-CTGCATGCACAGCAG---C------GTTGCGCCTTGGGCCG---------TATACCTCTCATTGACT--------------------------TGGGAGCGGTCTCAA-ATGACGA---ATCAGAGTCTC-----CTAGCG---AATGCACGGGCAAACGAAATATCCAGTAT----GGGACATAAA-T-C-GAGAGACGCAGCTCGATG-CA--CATGAAATGCGCTCCCGGGTTCCGATAAGTACTGATC-GTTCTGTCAGTTCGCAAATAAAAGATCCAATGTGAAG-TGATCAAACGGTGTAATGCTCTGTTCGGCAGAA----------------TTAATTTTTTGCC--TTTCACAC-- Mimachlamys_varia_2 ATAACATCTATCGCAAA-CTGCATGCACAGCAG---C------GTTGCGCCTTGGGCCG---------TATACCTCTCATTGACT--------------------------TGGGAGCGGTCTCAA-ATGACGA---ATCAGAGTCTC-----CTAGCG---AATGCACGGGCAAACGAAAAATCCAGTAT----GGAACATAAA-T-C-GAGAGACGCAGCTCGATG-CA--CATGAAATGCGCTCCCGGGTTCCGATAAGTACTGATC-GTTCTGTCAGTTCGCAAATAAAAGATCCAATGTGAAG-TGATCAAACGGTGTAATGCTCTGTTCGGCAGAA----------------TTAATTTTTTGCC--TTTCACAC-- Azumapecten_farreri AAAACATCTATCGCAAC-CTGCATGCACAGCAG---C------ATTGCGCCTTGGACCG---------TCTCGTCTCCCCG-------------------------------GCGAGCGGTCTTAA-ATGAGGA---ATCAGAGTCTC-----CAATCG---AACCAAAAACAAACCAGTACG-------------GAACAAATT-A-C-AAGAGACGCAGTTCGATT-AA-ACACAAAATGCGCTCTCGGTTCC--GTGAA-ACTGTAG-GTTCGCCT--TTTACATGTGAA--AAAAAAGGT---A-TGATGGT---GTAAATTTCTCTGGTCGACACAA-------------CACTTTGTGTTTGTCT--TTTCACAC-- Mizuhopecten_yessoensis AAAACATCTATCGCAAA-CTGCATGCACGTCAG---C------GTTGCGCCTTGGACCG---------TACATCTCCTCCTTACTTA----------------------AGGGGGAGCGGTCTCAA-ATGATGA---ATCAGAGTCTC-----CAAGCG---AACGTAGCAAAAACCCCGGTAAA-AAAAC----GGAACATTTA-A-C--AGAGACGCAGCTCGATG-CA---CAAACATGCGCTCTCAGTTTCCAAAAAGAAAGGGGGCGTTCAAT----------ATGA------AAATGT---G-AGAAAAT---ATAAAAGCTT----TCGGCACGT-------------T-TTGTTTTACGAGCC--TTTCACAC-- Mimachlamys_nobilis AAAACATCTATCGCAAA-CTGCGGGCACAGCAG---C------ATTGCGCCTTGGACCG---------TACATCTCATCTCCCCG--------------------------GGTGAGCGGTCCTAA-ATGACAA---ATCAGAGTCTC-----CAGGCA---AACGGTAAACACATCC-AGTA-------C----GGAACAAA---A-C--AGAGACGCAGCTCGGTTGC---TATGAATTGCGCTCC---------AAGTATCCGGGATTGTTGACC-----------TGAA----AATATGTTTGC-CAACTAGCAGGTGAATCAAAAATATTGACGAAA----------------TTTTTTTT--------CTCACTC-- Spondylus_gaederopous TGAATTTCCATCGCAGAGGCGTAGGCAAATGGCATGCCGCGCAACTGCGCCTTGGATCGAAAAACTTCCAACCCCCCCTTATTTGGGGGGTAGGGGAAGCGGTCCCAAGTTGAACAACGAACTTGCACTAACTGCTTTCGAGCGTTCGGGGTCTCGGCATATTTTGCCTCCGGCAACCGCAGTCGGAAAGTTGCCCGGGCGGGGCAGAC---GAGACGCAGGTCGGTG---ACAAAAACGTGCGCTCTC-------------GCCCGTCCATGAAAAA------------GGGTATACTCCCCGGGCTGTGCTCTGGGA-------------GCCGGCTGGTGGTCGAGATTTGTTCGACTCGCTCAAAGCA-TTTCTTTCTT ; options gapmode = newstate; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 383; END; BEGIN TREES; Title 'Trees from "ITS-2_def_MP.tre"'; LINK Taxa = Taxa; TRANSLATE 1 Pecten_jacobaeus_1, 2 Pecten_jacobaeus_2, 3 Pecten_maximus_1, 4 Pecten_maximus_2, 5 Pecten_keppelianus_1, 6 Pecten_keppelianus_2a, 7 Pecten_keppelianus_2b, 8 Pecten_novaezelandiae, 9 Amusium_pleuronectes, 10 Aequipecten_opercularis_2, 11 Aequipecten_opercularis_1, 12 Flexopecten_glaber_1, 13 Flexopecten_glaber_2, 14 Flexopecten_flexuosus, 15 Argopecten_irradians_, 16 Manupecten_pesfelis_1, 17 Manupecten_pesfelis_2, 18 Semipallium_fulvicostata, 19 Talochlamys_multistriata, 20 Talochlamys_pusio, 21 Mimachlamys_varia_1, 22 Mimachlamys_varia_2, 23 Azumapecten_farreri, 24 Mizuhopecten_yessoensis, 25 Mimachlamys_nobilis, 26 Spondylus_gaederopous; TREE PAUP_1 = (((((((1:0.0,2:1.0,3:0.0):11.0,4:10.0):41.0,(((5:0.0,6:0.0):1.0,7:0.0):2.0,8:1.0):52.0):50.0,9:93.0):75.0,(((10:1.0,11:0.0):24.0,(12:0.0,13:0.0,14:2.0):41.0):31.0,15:32.0):99.0):115.0,(((16:0.0,17:0.0):35.0,18:60.0):34.0,(((((19:4.0,20:3.0):95.0,(21:1.0,22:1.0):43.0):34.0,23:50.0):35.0,24:43.0):34.0,25:50.0):62.0):221.0):0.0,26:0.0); TREE PAUP_2 = ((((((1:0.0,2:1.0,3:0.0,4:1.0):52.0,(((5:0.0,6:0.0):1.0,7:0.0):2.0,8:1.0):52.0):50.0,9:93.0):75.0,(((10:1.0,11:0.0):24.0,(12:0.0,13:0.0,14:2.0):41.0):31.0,15:32.0):99.0):115.0,(((16:0.0,17:0.0):35.0,18:60.0):34.0,(((((19:4.0,20:3.0):95.0,(21:1.0,22:1.0):43.0):34.0,23:50.0):35.0,24:43.0):34.0,25:50.0):62.0):221.0):0.0,26:0.0); TREE PAUP_3 = (((((((1:0.0,2:1.0,3:0.0):10.0,4:9.0):41.0,((5:0.0,6:0.0):1.0,7:0.0,8:3.0):53.0):50.0,9:93.0):75.0,(((10:1.0,11:0.0):24.0,(12:0.0,13:0.0,14:2.0):41.0):31.0,15:32.0):99.0):115.0,(((16:0.0,17:0.0):35.0,18:60.0):34.0,(((((19:4.0,20:3.0):95.0,(21:1.0,22:1.0):43.0):34.0,23:50.0):35.0,24:43.0):34.0,25:50.0):62.0):221.0):0.0,26:0.0); TREE PAUP_4 = ((((((1:0.0,2:1.0,3:0.0,4:1.0):51.0,((5:0.0,6:0.0):1.0,7:0.0,8:3.0):53.0):50.0,9:93.0):75.0,(((10:1.0,11:0.0):24.0,(12:0.0,13:0.0,14:2.0):41.0):31.0,15:32.0):99.0):115.0,(((16:0.0,17:0.0):35.0,18:60.0):34.0,(((((19:4.0,20:3.0):95.0,(21:1.0,22:1.0):43.0):34.0,23:50.0):35.0,24:43.0):34.0,25:50.0):62.0):221.0):0.0,26:0.0); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 383; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 383; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1351165542560; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7470388383456517508; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 1017544999813145337; checksumv 0 2 1271862825 null numChars 383 short true bits 15 states 15 sumSquaresStatesOnly 146542.0 NumFiles 1 NumMatrices 1; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1440 792; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #7470388383456517508 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #7470388383456517508; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1340 725; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7470388383456517508 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 813.1351165104320.4273689573861893875; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1340 725; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 4; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #1017544999813145337 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1340 725; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; 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.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;