#NEXUS [written Wed Jun 03 00:50:43 PDT 2009 by Mesquite version 2.5+ (build j89) at Eupoa/192.168.1.100 (Rutger Vos)] BEGIN TAXA; TITLE M1000; DIMENSIONS NTAX=10; TAXLABELS Phytophthora_cinnamomi Phytophthora_vignae Phytophthora_cajani Phytophthora_melonis Phytophthora_sinensis 'Phytophthora drechsleri-like' Phytophthora_pistaciae_b Phytophthora_pistaciae_a Phytophthora_sojae_b Phytophthora_sojae_a ; IDS t0n0 t0n1 t0n2 t0n3 t0n4 t0n5 t0n6 t0n7 t0n8 t0n9 ; END; BEGIN CHARACTERS; TITLE M1000; DIMENSIONS NCHAR=835; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Phytophthora_cinnamomi CCACACCTAAAAAA-CTTTCCACGTGAACCGTTTCAACCCAATTAGTTGGGGGCCTGCTCTGGGCGGCGGT-TGTC-GATGTCAAAGTCGACGG-TTGCTGTTGCGTGGGGGGCCCTATCACTGGCGAGCG-TTTGGGTCCCCCTCG-GGGGAACTGAGCTAGTAGCCTCTCTTTTAAACCCATCCTGTAATACTGAACATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTGGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGGTGCCAGACGTGAGGTGTCTTGCGG-GCGGTCTTCGGACTGGCTGTGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGCTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCGGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTCCGATTCGCGGTATGGTTGGCTCCGGCTGAACAAAGCGCTTATTGGATGTTCCTCCCTGCTGTGGCGGTACGGATCGGTGAACCGTAGCTGTGCTAGGCTTGGCGTTTGAACCGGCGGTGTTGTTGCGAAGTAGGGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTCTGTGTCTCTCCGGCGCACTTGTGTGCTTGTGGTGGCATCTCAA Phytophthora_vignae CCACACCTAAAAAAACTTTCCACGTGAACCGTTTCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTAGCTGTC-GATGTCAAAGTCGGCGACTGGCTGCTATGTGACGGGCTCTATCA-TGGCAATTGGTTTGGGTCCTCCTCGTGGGGAACTAGATCATGAGCCCACTTTTTAAACCCATTCTTGATTACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGAGGTGTCTTGCGGCGCGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCAGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGCGGTATGGGCTGGTGAACCGTAGTTGTGCAAGGCTTGGCTTTTGAACCGGTGGTGTTGTTGCGAAGTAGGGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTTTGTGTTGTCTCTGCGGCTTGCTGTG---GAGGTAGCATCTCAA Phytophthora_cajani CCACACCTAAAAAA-CTTTCCACGTGAACCGTATCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTAGCTGTC-GATGTCAAAGTCGGCGACTGGCTGCTATGTGGCGGGCTCTATCA-TGGCAATTGGTTTGGGTCCTCCTCGTGGGGAACTAGATCATGAGCCCACTTTTTAAACCCATTCTTGATTACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGAGGTGTCTTGCGGCGCGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTCGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCAGTTTGTATGGTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGCGGTATGGGCTGGTGAACCGTAGTTGTGCAAGGCTTGGCTTTTGAACCGGTGGTGTTGTTGCGAAGTAGGGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGTG---GAGGTAGCATCTCAA Phytophthora_melonis CCACACCTAAAAAA-CTTTCCACGTGAACCGTATCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTAGCTGTC-GATGTCAAAGTCGGCGACTGGCTGCTATGTGGCGGGCTCTATCA-TGGCGATTGGTTTGGGTCCTCCTCGTGGGGAACTGGATCATGAGCCCACCTTTTAAACCCATTCTTGATTACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGAGGTGTCTTGCGGCGCGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCAGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGTGGTATGGGCTGGTGAACCGTAGTTGTGCGAGGCTTGGCTTTTGAACCGGCGGTGTTGTAGCGAAGTAGAGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGTG---GAGGTAGCATCTCAA Phytophthora_sinensis CCACACCTAAAAAA-CTTTCCACGTGAACCGTATCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTAGCTGTC-GATGTCAAAGTCGGCGACTGGCTGCTATGTGGCGGGCTCTATCA-TGGCGATTGGTTTGGGTCCTCCTCGTGGGGAACTGGATCATGAGCCCACCTTTTAAACCCATTCTTGATTACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGAGGTGTCTTGCGGCGCGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCAGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGTGGTATGGGCTGGTGAACCGTAGTTGTGCGAGGCTTGGCTTTTGAACCGGCGGTGTTGTAGCGAAGTAGAGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGTG---GAGGTAGCATCTCAA 'Phytophthora drechsleri-like' CCACACCTAAAAAA-CTTTCCACGTGAACCGTATCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTAGCTGTC-GATGTCAAAGTCGGCGACTGGCTGCTATGTGGCGGGCTCTATCA-TGGCGATTGGTTTGGGTCCTCCTCGTGGGGAACTGGATCATGAGCCCACCTTTTAAACCCATTCTTGATTACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGAGGTGTCTTGCGGCGCGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCAGTTTGTCTGCTGCGGCGTTTAATGAAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGTGGTATGGGCTGGTGAACCGTAGTTGTGCGAGGCTTGGCTTTTGAACCGGCGGTGTTGTAGCGAAGTAGAGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGTG---GAGGTAGCATCTCAA Phytophthora_pistaciae_b CCACACCTAAAAAA-CTTTCCACGTGAACCGCATCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTGGCTGTC-GATGTCAAAGTCGGCGGCTGGCTGCTATGTGGCGGGCTCTATCA-TGGCGATTGGTTTGGGTCCTCCTCGTGGGGAACTGGATCATGAGCCCACTTTTTAAACCCATTCTTGATTACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGGGGTGTCTTGCGGCGCGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTAAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCAGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGCGGTATGGGCTGGTGAACCGTAGCTGTGCGAGGCTTGGCTTTTGAACCGGCGGTGTTGTTGCGAAGTAGGGTGGCGGCTTCGGCTGTCGAGAGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGCG---GAGGTGGCATCTCAA Phytophthora_pistaciae_a CCACACCTAAAAAA-CTTTCCACGTGAACCGCATCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTGGCTGTC-GATGTCAAAGTCGGCGGCTGGCTGCTATGTGGCGGGCTCTATCA-TGGCGATTGGTTTGGGTCCTCCTCGTGGGGAACTGGATCATGAGCCCACTTTTTAAACCCATTCTTGATTACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGGGGTGTCTTGCGGCGCGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTAAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCAGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGCGGTATGGGCTGGTGAACCGTAGCTGTGCGAGGCTTGGCTTTTGAACCGGCGGTGTTGTTGCGAAGTAGGGTGGCGGCTTCGGCTGTCGAGAGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGCG---GAGGTGGCATCTCAA Phytophthora_sojae_b CCACAACTAAAAAA---TTCCACGTGAACCGTATCAAC--AAGTAGTTGGGGGGCTGCTCTGTGTGGCTGTCTGTC-GATGTCAAAGTCGGCGGCTGGCTGCTGTGTGGCGGGCTCTATCA-TGGCGATTGGTTTGGGTCCTCCTCGTGGGGAACTGGATCATGAGCCCACTTTTTAAACCCATTCTTAAATACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGAGGTGTCTTGCGGCGTGGCCTTCGGCCTGCCTGCGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGCCTGCCTGTATGGCCAGTCGGCGACCGGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGCGGTATGAGCTGGTGAACCGTAGCTGTGTGAGGCTTGGCTTTTGAACCGGCGGTGTTGTTGCGAAGTAGGGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGCG---GAG--TGCATCTCAA Phytophthora_sojae_a CCACACCTAAAAAA-CTTTCCACGTGAACCGTATCAAC--AAGTAGTTGGGGGCCTGCTCTGTGTGGCTGTCTGTCCGACGTCAAAGTCGGCGGCTGGCTGCTGTGTGGCGGGCTCTATCA-TGGCGATTGGTTTGGGTCCTCCTCGTGGGGAACTGGATCATGAGCCCACTTTTTAAACCCATTCTTAAATACTGAATATACTGTGGGGACGAAAGTCTCTGCTTTTAACTAGATAGCAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTTAGTCCTGGGAGTATGCCTGTATCAGTGTCCGTACATCAAACTTGGCTCTCTTCCTTCCGTGTAGTCGGTGGATGGAGACGCCAGACGTGAGGTGTCTTGCGGCGTGGCCTTCGGGCTGCCTGCGAGTCCCTTGAAATGTACTGAACTGTACTTCTCTTTGCTCGAAAAGCGTGACGTTGTTGGTTGTGGAGGCTGCCTGTATGGCCAGTCGGCGACCGGTTTGTCTGCTGCGGCGTTTAATGGAGGAGTGTTCGATTCGCGGTATGGTTGGCTTCGGCTGAACAATGCGCTTATTGGATGCTTTTCC-TGCTGTGGCGGTATGGGCTGGTGAACCGTAGCTGTGTGAGGCTTGGCTTTTGAACCGGCGGTGTTGTTGCGAAGTAGGGTGGCGGCTTCGGCTGTCGAGGGTCGATCCATTTGGGAACTCTGTGTTGTCTCTGCGGCTTGCTGCG---GAGGTGGCATCTCAA ; BLOCKID c0; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 835; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 835; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 835; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8012473894217097228; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6026245562618207952 c0; checksum 0 1905949690 c0; endTell; getWindow; tell It; setResourcesState false false 175; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 269 143; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8012473894217097228 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8012473894217097228; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 525 397; setLocation 269 143; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #6026245562618207952 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 525 397; setLocation 269 143; 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; 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; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #6026245562618207952 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; newAssistant #mesquite.lists.CharListCodonPos.CharListCodonPos; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 525 397; setLocation 269 143; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;