#NEXUS [written Wed Jul 20 10:33:19 EDT 2011 by Mesquite version 2.73 (build 544) at ComPhy.local/10.0.1.3] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=5; TAXLABELS Halodule_pinifolia_YI01241 Halodule_uninervis_YI01240 Halodule_wrightii_YI01254 Potamogeton_maackianus_Pm052 Ruppia_megacarpa_MED01 ; END; BEGIN CHARACTERS; TITLE Halodule_phyB; DIMENSIONS NCHAR=1050; FORMAT DATATYPE = DNA GAP = - MISSING = -; MATRIX Halodule_pinifolia_YI01241 AGGCTGCAAGCTCTGCCCGGTGGAGACATCAAGCTTCTCTGTGACACGGTCGTGGAGCATGTCAGGGAACTCACTGGGTACGACAGGGTAATGGTCTATAGGTTCCACGAGGACGAGCATGGGGAAGTTGTTGCAGAGAGCAAAAGAGGTGATATGGAGCCGTATATTGGTCTCCATTACCCCGCCACCGACATACCCCAGGCCTCGAGGTTCCTGTTTAAACAGAATAGGGTGAGGATGATTGCTGATTGCCGGGCAACCCCCATCCGGATGATACAAGATGAGAGCCTGATGCAGCCACTTTGCCTCGTAGGATCCACACTGCGAGCTCCACATGGTTGTCATGCGCAATACATGGCCAACATGGGCTCGATCGCCTCCCTTGCCATGGCTGTTATCATTAATGGGTGTGAAGAAGAGGGTACAAGGAATTCTATGAAGTTATGGGGCCTTGTTGTCTGTCACCATGCTTCTCCGAGATGCATTCCATTTCCGCTGCGCTATGCCTGTGAGTTCCTCATGCAAGCATTTGGCCTTCAGCTGAATATGGAGCTTCAGCTGGCATCCCAGTTGTCCGAGAAGCACATCTTGAGAACTCAGACCCTTCTCTGTGACATGCTTCTTCGGGACTCTCCTACTGCACTTGTCACGCAGAGCCCTAGCATAATGGATCTCGTGAGGTGCGATGGTGCTGCGCTGTATTACCAGGGAAAGTATTGGCCTCTTGGTGTCACCCCTTCTGAAGCAGAGATTAAAGGTATTGTTGGGTGGTTGTTAGCTAGTCATGGAGACTCCACAGGCTTGAGCACAGACAGTCTGGCCGATGCAGGCTATCCGGGCGCTGCGTCCCTTGGGGATGCAGTTTGTGGTATGGCGGTGGCTCACATCACCCCCGTAGACTTCTTGTTTTGGTTCAGGTCACACACAGCAAAAGAGATAAAATGGGGCGGTGCAAAACATCATCCTGGAGACAAGGATGATGGGCAGCGTATGCATCCTCGTACATCTTTTAGTGCTTTTCTAGAAGTTGTGAAAAGTAGGAGTCTTCCA Halodule_uninervis_YI01240 AGGCTGCAAGCTCTGCCCGGTGGAGACATCAAGCTCCTCTGTGACACGGTCGTGGAGCATGTCAGGGAACTCACTGGGTACGACAGAGTAATGGTCTATAAGTTCCACGAGGACGAGCATGGGGAAGTTGTTGCAGAGAGCAAAAGAGGTGATATGGAGCCGTATATTGGTCTCCATTACCCCGCCACCGACATACCCCAGGCCTCGAGGTTCCTGTTTAAACAGAATAGGGTGAGGATGATTGCTGATTGCCGGGCAACCCCCATCCGGATGATACAAGATGAGAGCCTGATGCAGCCACTCTGCCTCGTAGGATCCACACTGCGAGCTCCACACGGTTGTCATGCGCAATACATGGCCAACATGGGCTCGATCGCCTCCCTTGCCATGGCTGTTATCATTAATGGGTGTGAAGAAGAGGGTACAAGGAATTCCATGAAGTTATGGGGCCTTGTTGTCTGTCACCATGCTTCTCCGAGATGCATTCCATTTCCGCTGCGCTATGCCTGTGAGTTCCTCATGCAAGCATTTGGCCTTCAGCTGAATATGGAGCTTCAGCTGGCATCCCAATTGTCCGAGAAGCACATCTTGAGAACTCAGACCCTTCTCTGTGACATGCTTCTTCGGGACTCTCCTACTGCACTTGTCACGCAGAGCCCTAGCATAATGGATCTCGTGAGGTGCGATGGTGCTGCGCTGTATTACCAGGGAAAGTATTGCCCTCTTGGTGTCACCCCTTCTGAAGCAGAGATTAAATGTATTGTTGGGTGGTTGTTGGCTAGTCATGGAGACTCCACAGGCTTGAGCACAGACAGTCTGGCCGATGCAGGCTATCCGGGCGCTGCGTCCCTTGGGGATGCAGTTTGTGGTATGGCGGTGGCTCACATCACCCCCGTAGACTTCTTGTTTTGGTTCAGGTCACACACAGCAAAAGAGATAAAATGGGGCGGTGCAAAACATCATCCTGGAGACAAGGATGATGGGCAGCGTATGCATCCTCGTACATCTTTTAGTGCCTTTCTAGAAGTTGTGAAAAGTAGGAGCCTTCCA Halodule_wrightii_YI01254 AGGCTGCAAGCTCTGCCCGGTGGAGACATCAAAATCCTCTGTGACACTGTCGTGGAGCACGTCAGGGAGCTCACTGGGTACGACAGGGTAATGGTCTACAAATTCCACGAGGACGAGCATGGGGAAGTTGTTGCCGAGAGCAAAAGTGATGACATGGAGCCGTATATAGGTCTCCATTACCCCGCCACCGACATACCCCAGGCCTCTAGGTTCCTGTTTAAACAGAATAGGGTGAGGATGATCGCTGATTGCCGAGCAACGCCCATCCGGATGATACAAGATGAGAACCTGATGCAGCAACTCTGCCTCGTAGGATCCACACTGCGAGCTCCGCACGGTTGTCATGCGCAATACATGGCCAACATGGGCTCGATCGCCTCCCTTGCCATGGCTGTTATAATTAATGGCGGTGAAGATGAGGGTACAAGGAATTCCATGAAGTTATGGGGCCTTGTTGTCTGTCACCATGCTTCTCCGAGATGCATTCCATTTCCGCTGCGCTATGCTTGTGAGTTCCTCATGCAGGCATTTGGCCTTCAGCTAAATATGGAGCTTCAGCTGGCATCCCAATTTTCCGAGAAGCACATCTTGAGAACTCAGACCCTTCTCTGTGACATGCTTCTTCGGGACTCTCCTACTGCACTTGTCACGCAGAGCCCTAGCATAATGGATCTTGTGAGGTGCGATGGTGCTGCGCTGTATTACCAGGGAAAGTATTGGCCTCTTGGTGTCACCCCTTCTGAAGCTCAGATTAAAGATATTGTTGGGTGGTTGTTAGCTAGTCATGGAGACTCCACAGGCTTGAGCACAGACAGTCTGGCCGATGCTGGCTATCCGGGTGCTGCGTGCCTTGGGGATGCAGTTTGTGGTATGGCGGTGGCTTACATTACCCCCGTAGACTTCTTGTTTTGGTTCAGATCACACACAGCAAAAGAGATAAAATGGGGCGGTGCAAAACATCATCCTGGAGACAAGGATGATGGCCAGCGTATGCATCCTCGTACATCTTTTAGTGCCTTTCTAGAAGTTGTGAAAAGTAGGAGCCTTCCA Potamogeton_maackianus_Pm052 AGGTTGCAGGCGCTGCCTGGTGGGGATATCAATCTTTTATGTGACACAGTTGTGGACCATGTTAGGGAACTCACAGGATATCACAGGGTCATGGTCTACAAGTTCCATGAGGATGAACATGGCGAGGTTGTTGCAGAGAGTAAAAGGGACGACTTAGAACCATATATGGGTCTTCACTACCCTGCCACAGATATACCCCAAGCCTCAAGATTCTTGTTCAAACAAAATAGAGTTAGGATGATAGCAGATTGTCGTGCAACCCCTGTTCGAGTCATACAAGATGAGAATCTGATGCAACCACTTTGCCTTGTGGGTTCCACTCTACGAGCTCCCCATGGTTGCCATGCACAGTATATGGCCAACATGGGATCAATTGCATCTCTTGCCATGGCTGTAATTATCAATGGAGGTGAAGAAGAGGGTACGAAGAACTCGATGAAGTTATGGGGTCTCGTTGTTTGTCACCACACTTCTCCGAGGTTCATACCCTTCCCATTGCGGTATGCATGCGAGTTCCTTATGCAGGCTTTTGGCCTTCAGTTGAATATGGAACTCCAGTTGGCCTCCCAAATGTCTGAGAAGCATATCTTGAGAACCCAGACCCTTTTGTGCGATATGATCCTTCGAGATTCACCTACTGGAATTGTCACACAAAGCCCTAGCATAATGGATCTTGTGAAGTGTGACGGCGCAGCGCTTTATTACCATGGAAAGTATTGGCCACTAGGTGTAACTCCTTCAGAATCACAAATTAAGGATATCGTGGAATGGCTGTTGGCAACCCACGGAGACTCCACAGGCCTGAGCACAGATAGTTTGGCTGATGCCGGATACCCTAGTGCTGCATCACTTGGTGATGCTGTTTGTGGTATGGCTGTGGCTTACATCACATCAAGAGATTTCTTGTTTTGGTTTAGATCCCACACAGCTAAAGAGGTTAAGTGGGGTGGTGCAAAACATCACCCTGAAGACAAGGATGATGGGCAGCGGATGCATCCTCGGACATCTTTTAATGCTTTCCTCGAAGTAGTGAAAAGTGAGAGCCTTCCG Ruppia_megacarpa_MED01 CGGTTACAGGCTTTGCCAGGTGGAGATATTAAGTTTCTGTGTGACACAGTTGTGGACCATGTTAGGGAACTCACTGGATATGATAGGGTTATGGTCTACAAGTTCCATGAGGATGAGCATGGGGAAGTTCTTGCTGAGAGTAAAAGAAGTGACTTGGAACCGTATATAGGTCTCCATTACCCTGCCACAGACATACCCCAAGCCTCAAGGTTCTTATTTAAACAGAACAGAGTTAGGATGATAGCTGATTGTCGTGCAACTCCTGTTAGCATGATACAAGATGAGAACCTGATGCAGCCACTTTGCCTTGTAGGATCCACACTACGAGCTCCTCATGGCTGCCATGCACAATACATGGCTAACATGGGGTCAGTTGCTTCTCTTGTTATGGCTGTTATCATTAATGGGGGAGAAGAAGACGGCACAAGGAACTCTATGAAGCTATGGGGCCTTGTTGTTTGCCACCATACTTCTCCCAGATGCATTCCATTTCCATTGCGCTATGCCTGTGAGTTCCTCATGCAGGCTCTAGGCCTTCAGCTTAATATGGAAGTTCAGTTGGCTGCCCAGATGTCTGAAAAACACATATTAAGAACTCAAACCCTTTTATGTGATATGCTTCTTCGTGATTCTCCTACTGGAATTGTTACACAAAGTCCGAGTATAATGGACCTTGTGAAGTGTGATGGCGCGGCACTCTATTACCATGGTAAGTATTGGCCACTCGGTGTTGCCCCTTCTGAGGAAAAAATTAAAGATATCATTGGCTGGTTATTGGCAAGTCATGGAGACTCCACGGGCTTGAGCACAGATAGTTTGGCGGATGCTAGCTACCCAGGTGCCGCTTCCCTTGGGGATGCAGTTTGTGGCATGGCAGTGGCATATATCACCTCAAGAGATTTTTTGTTTTGGTTTAGATCCCATACTGCAAAAGAAATAAAGTGGGGTGGTGCTAAACATCATCCTGAAGACAAAGACGATGGACAGCGTATGCATCCCCGCACATCTTTTAATGCCTTCCTGGAAGTTGTGAAAAGTAGGAGCCTTCCA ; END; BEGIN TREES; Title Halodule_phyB_MP; LINK Taxa = Taxa; TRANSLATE 1 Halodule_pinifolia_YI01241, 2 Halodule_uninervis_YI01240, 3 Halodule_wrightii_YI01254, 4 Potamogeton_maackianus_Pm052, 5 Ruppia_megacarpa_MED01; TREE PAUP_1 = ((5:79.0,(2:23.0,1:27.0,3:23.0):96.0):46.0,4:46.0); END; BEGIN TREES; Title Halodule_phyB_MB; LINK Taxa = Taxa; TRANSLATE 1 Halodule_pinifolia_YI01241, 2 Halodule_uninervis_YI01240, 3 Halodule_wrightii_YI01254, 4 Potamogeton_maackianus_Pm052, 5 Ruppia_megacarpa_MED01; TREE con_50_majrule = ((5:0.095511,(2:0.018228,1:0.021934000000000002,3:0.028475)0.98:0.131345)1.00:0.074132,4:0.074132); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 1050; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 1050; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1050; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1311172399704; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8657303074091441972; tell It; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4970126051123504943; tell It; attachments ; endTell; mqVersion 273; checksumv 0 2 2954235859 null getNumChars 1050 numChars 1050 getNumTaxa 5 numTaxa 5 short true bits 15 states 15 sumSquaresStatesOnly 116547.0 sumSquares 116547.0 NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 272; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 922 664; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.trees.ManageTrees.ManageTrees; tell It; getTreeBlock 0; tell It; attachments ; endTell; getTreeBlock 1; tell It; attachments ; endTell; endTell; endTell; end;