#NEXUS [written Mon Mar 18 17:47:15 EDT 2013 by Mesquite version 2.74 (build 550) at cesar-herreras-MacBook-Pro.local/10.109.194.193] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=27; TAXLABELS Pseudocosmospora_eutypellae_AR4453 Pseudocosmospora_eutypellae_AR4527 Pseudocosmospora_eutypellae_AR4562 Pseudocosmospora_eutypellae_CH1002 Pseudocosmospora_eutypellae_GJS10248 Pseudocosmospora_eutypellae_GJS9315 Pseudocosmospora_sp_AR4768 Pseudocosmospora_rogersonii_CH1011 Pseudocosmospora_rogersonii_GJS9056 Pseudocosmospora_sp_MAFF241531 Pseudocosmospora_rogersonii_CH1012 Pseudocosmospora_rogersonii_GJS091384 Pseudocosmospora_sp_CH1102 Pseudocosmospora_sp_MF241499 Pseudocosmospora_vilior_AR4771 Pseudocosmospora_sp_GJS96216 Pseudocosmospora_vilior_AR4810 Pseudocosmospora_vilior_PC1246 Pseudocosmospora_eutypae_CH1101 Pseudocosmospora_eutypae_IM73016 Pseudocosmospora_sp_GJS95141 Pseudocosmospora_sp_AR4826 Pseudocosmospora_metajoca_AR4576 Pseudocosmospora_joca_AR4779 Pseudocosmospora_sp_GJS95143 Microcera_larvarum_AR4580 Corallomycetella_repens_AR4547 ; END; BEGIN CHARACTERS; TITLE TEF; DIMENSIONS NCHAR=280; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Pseudocosmospora_eutypellae_AR4453 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacaaa---tcctttttacccctcctttggcggaaaaaaaaagc---aaatttccatttcctt---tggccccacttcctgcttcgagttctctaggtgggtgggtggtgtggtgtggtcttaccccgctacctgccagacgtcgcaatttttgccctgcttccactcgtgattctgcctttattctc--------------tggcttcgcgttgatgaattgaaaactcgttgctaacaac Pseudocosmospora_eutypellae_AR4527 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacaaa---tcctttttacccctcctttggcggaaaaaaaaagc---aaatttccatttcctt---tggccccacttcctgcttcgagttctctaggtgggtgggtggtgtggtgtggtcttaccccgctacctgccagacgtcgcaatttttgccctgcttccactcgtgattctgcctttattctc--------------tggcttcgcgttgatgaattgaaaactcgttgctaacaac Pseudocosmospora_eutypellae_AR4562 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacaaa---tcctttttacccctcctttggcggaaaaaaaaagc---aaatttccatttcctt---tggccccacttcctgcttcgagttctctaggtgggtgggtggtgtggtgtggtcttaccccgctacctgccagacgtcgcaatttttgccctgcttccactcgtgattctgcctttattctc--------------tggcttcgcgttgatgaattgaaaactcgttgctaacaac Pseudocosmospora_eutypellae_CH1002 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacaaa---tcctttttacccctcctttggcggaaaaaaaaagc---aaatttccatttcctt---tggccccacttcctgcttcgagttctctaggtgggtgggtggtgtggtgtggtcttaccccgctacctgccagacgtcgcaatttttgccctgcttccactcgtgattctgcctttattctc--------------tggcttcgcgttgatgaattgaaaactcgttgctaacaac Pseudocosmospora_eutypellae_GJS10248 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacaaa---tcctttttacccctcctttggcggaaaaaaaaagc---aaatttccatttcctt---tggccccacttcctgcttcgagttctctaggtgggtgggtggtgtggtgtggtcttaccccgctacctgccagacgtcgcaatttttgccctgcttccactcgtgattctgcctttattctc--------------tggcttcgcgttgatgaattgaaaactcgttgctaacaac Pseudocosmospora_eutypellae_GJS9315 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacaaa---tcctttttacccctcctttggcggaaaaaaaaagc---aaatttccatttcctt---tggccccacttcctgcttcgagttctctaggtgggtgggtggtgtggtgtggtcttaccccgctacctgccagacgtcgcaatttttgccctgcttccactcgtgattctgcctttattctc--------------tggcttcgcgttgatgaattgaaaactcgttgctaacaac Pseudocosmospora_sp_AR4768 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pseudocosmospora_rogersonii_CH1011 tcgctcgaatcgacctcgtcgttcgctgccctcgaaaccacacaa--tcctttttacccctcctttggcgaaaaaaaaaac----aaatttccatttcctt---tggccccacttcctgcttcgagtcctcttggtgggtgggtggtg-----tggtcttaccccgctacctacaagacgtcgcaatttttgcactgcttccactcgtgattctgctttttttcct------------ctggcctccgcgctcaagaattacaaacctgatgctaacaac Pseudocosmospora_rogersonii_GJS9056 tcgctcgaatcgacctcgtcgttcgctgccctcgaaaccacacaa--tcctttttacccctcctttggcgaaaaaaaaaac----aaatttccatttcctt---tggccccacttcctgcttcgagtcctcttggtgggtgggtgg-g-----tggtcttaccccgctacctacaagacgtcgcaatttttgcactgcttccactcgtgattctgctttttttcct------------ctggcctccgcgctcaagaattacaaacctgatgctaacaac Pseudocosmospora_sp_MAFF241531 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacacaa--tcctttttacccctcctttggcggaaaaaaaaaac---aaatttccatttcctt---tggccccacttcctgcttcgagtcctcttgggggggggg----------gggtcttaccccgctacctgcaa-acgtcgcgattttggccctgcttccactcatggctctgccttttttttc-----------tctggcctccgcgtccaacaattgaaaacctgatgctaacaac Pseudocosmospora_rogersonii_CH1012 tcgctcgaatcgacctcgtcgttcgctgccctcgaaaccacacaa--tcctttttacccctcctttggcgaaaaaaaaaac----aaatttccatttcctt---tggccccacttcctgcttcgagtcctcttggtgggtgggtggtg-----tggtcttaccccgctacctacaagacgtcgcaatttttgcactgcttccactcgtgattctgctttttttcct------------ctggcctccgcgctcaagaattacaaacctgatgctaacaac Pseudocosmospora_rogersonii_GJS091384 tcgctcgaatcgacctcgtcgttcgctgccctcgaaaccacacaa--tcctttttacccctcctttggcgaaaaaaaaaac----aaatttccatttcctt---tggccccacttcctgcttcgagtcctcttggtgggtgggtggtg-----tggtcttaccccgctacctacaagacgtcgcaatttttgcactgcttccactcgtgattctgctttttttcct------------ctggcctccgcgctcaagaattacaaacctgatgctaacaac Pseudocosmospora_sp_CH1102 ---gtcgattcgacctcgtcggtcgttgccctcgaaaccacacaa--tcctccttacccctccttcagcgaaaaaaaaaaca---aaattcccgtttcctc---aggccccacttcttgcttcgagtcctcttagcgggggtgg---------tggtcttaccccgccacctggaagacattgttatttgcgct---gccccatta-----tctgcccttttctggccgctcttg--gctgcacatcgtctcgatgaactggaaacatgatgc------- Pseudocosmospora_sp_MF241499 tcgctcgaatcgacctcgtcgttcgttgccctcgaaaccacacaat-ccttttttacccctcctttggcggaaaaaaaaaac---aaagtaccatttcctt---tggccccacttcctgcttcgagttctcttggtgggtggggg--------gggtcttaccccgctacctgccagacgtcgcaatttttgccctacttccactcgtgattctgccttttttctc--------------tgggttcgcgttgatgaattgaaaactcgttgctaacaac Pseudocosmospora_vilior_AR4771 gtcgtcgattcgacctcgtcgtccgttgccctcgagaccacacaa--tcct-cttacccctccttcgccggaaaaaaaaacacagaaaaatccatctgctt---gggccccactccttacttccagtgcttgtggtgggg-------------tttcatgatcccgccacctgcct---------------------gccccactagtcatttcacaagccgccgcctcgcccat-tgatacttgg-tatccgatcagggagggacacttatctgact-- Pseudocosmospora_sp_GJS96216 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pseudocosmospora_vilior_AR4810 gtcgtcgattcgacctcgtcgttcgttgccctcgagaccacataa--tcct-cttacccctccttcggcggaaaaaaaaacacagaaaaatccattt-ctt---gggccccactccttgctttcagtgcctgtggtggga-------------tttcatgaccccgccatctgcct---------------------gccccactagtcatttcgcaagccgccgcctcgcccat-tgatactttgatatacgatcagtgagagacttgtatctgact-- Pseudocosmospora_vilior_PC1246 gtcgtcgattcgatctcgtcgtcccttgccctcgagaccacacaa--tcct-cttacccctccttcgccgg--aaaaaaacacagaaaaatccatctgctt---gcgccccactccttgcttccagtgcctgtggtgggg-------------tttcatgaccccgccacctgcct---------------------gccccacttgtcatttcgcaagccgccgcctcgcccat-cgatacttgg---tatctctagtgagagacacttatctgact-- Pseudocosmospora_eutypae_CH1101 tccctgaactcgacctcgtcgttcgttgcccctcgaaacccacacttttttccttgcccctcccaccg-----agaaaaagcgaaaatattttttcatgggagggggctccactacttgttgatggtgatagtggg-----------------gtggtttaccccgccacctgcacgagt-----------------tgcacactctaccctcagcagcggcttcgccttctccagcccgcagcacatgtttgtcaacgcaaaatcccgaggctgatcat Pseudocosmospora_eutypae_IM73016 tccctgaactcgacctcgtcgttcgttgcccctcgaaacccacacttttttccttgcccctcctcccaccgaaaaaaaaagcgaaaatattttttcatgggagggggctccactacttgttgatggtgatagtggg-----------------gtggtttaccccgccaccagcacgagt-----------------tgcacactctacccttagcagcggcttcgccttctccagcccgcagcacatgtttgtcaacgcaaaatcccgaggctgatcat Pseudocosmospora_sp_GJS95141 ttcgtcgattcgacctcgtcgttcattgccctcgaggccacacaa--ttctctttacccctccttcagcgaaaaaaaaaacat--aaaattccctttcttcccgaggccccacttcctgcttcgagtccttctctctagcgggtgg-------tggtcttaccccgccacctgcaagacgttgcaattttgtct---gccccactaccaattttgccctttccggccgctcccaa--gctgcacatctccccgatgagtcggaaccatgatgctaactct Pseudocosmospora_sp_AR4826 tctgccggttcgaccttagcgatcgttgccctcgaaaccactccc-tcttcctttacccctcccttggtgggaaaaattagg---aaaaccaattttccct---tggccccacttctttggtccagtgtgagcgcttgggtatcgagggg---ttatacaaccccaccatcggcccaaacatgtcgccgccaggccttgctcagtcgcagattcacatgggtgtct-----------------------tttctttggagagagactgataactgactt- Pseudocosmospora_metajoca_AR4576 tgcgtcgattcgacctcatcgctcgttaccctcgagaccgcacaa--acacgtttacccctcctcccgcgagaaaaaaaaaa----------catttttgc---gcgccccacttcttatttcgactggttttggtgggg-------------tgtttctaccccgccacctgctcgaggttgcaatttgctca---gccccaccagcgccagcgcctgcactcttgcggcctcatcccatcccagctcatcgacgtatcgg--tcagtatgctaactgt Pseudocosmospora_joca_AR4779 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pseudocosmospora_sp_GJS95143 ttcgtcgattcgacctcgtcgttcgttgcccacgaaaccacacaa-----tccttacccctcatttggcggaaaaaaaataca--aaaatcccattttctt---aggccccacttcttgcttcgagtcctccttgagggggacctggtggtggttctcttaccccgccacctgcaagacgtt-caatttgccct---gacccactcccaattctgccctctgccgccgctccaaaaagcacatcatcgcatcgttga----------------------- Microcera_larvarum_AR4580 cccatcgatccgactccgtcgctcgttgcactctcgaagcactgc--acctgttgtcccctccca--------------------caaacaaaattttcca---atgccccattaatt--------tttttttggtggg--------------gcagtttaccccgccacccagcagacgtcgtagtcttgccctgccccacaatcactgccttcaaagagcttcaccatcagccttgttccacgtcttgttg---------aaacacaatgctaacat- Corallomycetella_repens_AR4547 gtcgt----------------ttcgctgcgatatcaacacaatgccacctgtgcaacccctcctctccctcgaaccaaaa-------------attttctc---gggcccataatttt----------ttcttggtggg--------------ggttgctaccccgccacctggctgaggttgcatcttgcacc---gccccactagccacctcttctcgattcggcagtccccaacacatatcgcatcgaaccctcgagaggagcatggcgctgacagt ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 280; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 280; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 280; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1363643235277; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7269866726743197583; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8520121513077576307; mqVersion 274; checksumv 0 2 3664293785 null getNumChars 280 numChars 280 getNumTaxa 27 numTaxa 27 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 136157.0 sumSquares 7.90904152160297E20 NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #8520121513077576307 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; togglePaleInapplicable on; toggleShowBoldCellText 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.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; 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;