#NEXUS [written Wed Aug 26 10:44:10 BRT 2015 by Mesquite version 3.04 (build 725) at fernando-HP-Pavilion-15-Notebook-PC/127.0.1.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=13; TAXLABELS 'Caldanaerobacter subterraneus pacificus_CDSM653_0931' 'Caldanaerobacter subterraneus yonseiensis_ERM93008.1' 'Caldanaerobacter subterraneus tengcongensis_NP_622544.1' 'Thermoanaerobacter sp. YP_001663748.1' 'Thermoanaerobacter wiegelii YP_004819691.1' 'Thermoanaerobacter italicus YP_003476668.1' 'Thermoanaerobacter pseudethanolicus YP_001665444.1' 'Thermoanaerobacterium thermosaccharolyticum YP_007298419.1' 'Thermoanaerobacterium xylanolyticum YP_004471285.1' 'Thermoanaerobacterium saccharolyticum YP_006392731.1' 'Thermoanaerobacterium thermosaccharolyticum YP_003851722.1' 'Coprothermobacter proteolyticus YP_002246549.1' 'Coprothermobacter platensis WP_018962527.1' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=649; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX 'Caldanaerobacter subterraneus pacificus_CDSM653_0931' -----------MKTLEELERIRKETLEKINLRK-DRSG--VRIAVGMATCGIAAGARQVMMAILDELAKRNVTN-VLVTETGCIGMCKLEPIVDVYMPGQEKVTYVKVDEKKARQIVVEHVINGHPIREWTIENYE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Caldanaerobacter subterraneus yonseiensis_ERM93008.1' -----------MKTLEELERIRKETLEKINLRK-DRSG--VRIAVGMATCGIAAGARQVMMAILDELAKRNVTN-VLVTETGCIGMCKLEPIVDVYMPGQEKVTYVKVDEKKARQIVVEHVINGHPIREWTIENYE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Caldanaerobacter subterraneus tengcongensis_NP_622544.1' -----------MKTLEELERIRKETLEKINLRK-DRSG--VRIAVGMATCGIAAGARQVMMAILDELAKRNVTN-VLVTETGCIGMCKLEPIVDVYMPGQEKVTYVKVDEKKARQIVVEHVINGHPIREWTIENYE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter sp. YP_001663748.1' -----------MKSIEELERIRKETLEKINLRK-DRSG--IRIAVGMATCGIAAGARPVMMAILDELSKRNVTD-VIVTETGCIGMCKLEPIVDVYVPGQEKVTYVKVDEKKARQIVVEHVINGHPIREWTIENYE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter wiegelii YP_004819691.1' -----------MKSIEELEKIRKETLEKINLRK-DRSG--IRIAVGMATCGIAAGARPVMMAILDELSKRNVTD-VIVTETGCIGMCKLEPIVDVYVPGQEKVTYVKVDEKKARQIVVEHVINGHPIREWTIENYE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter italicus YP_003476668.1' -----------MKSIEELEKIRKETLERINLRK-DRSG--VRIAVGMATCGIAAGARPVMMAILDELSKRNVTD-VIVTETGCIGMCKLEPIVDVYVPGQEKVTYVKVDEKKARQIVAEHVINGHPIREWTIENYE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter pseudethanolicus YP_001665444.1' -----------MKSIEELEKIRKETLGKINLRK-DRSG--IRIAVGMATCGIAAGARPVMMAILDELSKRNVTD-VIVTETGCIGMCKLEPIVDVYVPGQEKVTYVKVDEKKARQIVVEHVINGHPIREWTIENYE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium thermosaccharolyticum YP_007298419.1' -----------MKSIEELEKIRRETLEKVNLRK-DRNG--IRITVGMATCGIAAGARPVMMAILDELGKRNITD-VVVAETGCIGMCKYEPMVDVYIPGQEKVTYIKVDENKARQIIAEHVVNGHPIKEWTISNVE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium xylanolyticum YP_004471285.1' -----------MKSIEELEKIRKETLEKVNLRK-DRNG--IRITVGMATCGIAAGARPVMMAILDELGKRNITD-VVVAETGCIGMCKYEPMVDVYVPGQEKVTYIKVDENKARQIVAEHVVNGHPIKEWTISSIE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium saccharolyticum YP_006392731.1' -----------MKSIEELEKIRKETLEKVNLRK-DRNG--IRITVGMATCGIAAGARPVMMAILDELGKRNITD-VVVAETGCIGMCKYEPMVDVYVPGQEKVTYIKVDENKARQIVAEHVVNGHPIKEWTISSVE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium thermosaccharolyticum YP_003851722.1' -----------MKSIEELEKIRKETLEKVNLRK-DRNG--IRITVGMATCGIAAGARPVMMAILDELGKRNITD-VVVAETGCIGMCKYEPMVDVYIPGQEKVTYIKVDENKARQIIAEHVVNGHPIKEWTISSVE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Coprothermobacter proteolyticus YP_002246549.1' --------MKQIKTLEDLQKIREEALRKVNIRS-DRSG--TRITVGMATCGIAAGARPVMMAILDELEKRNVTG-VTVVETGCIGLCKFEPIVEVYVPGHEKVTYIKMDPDKARQVVVEHVINGHPIREWTLESAELE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Coprothermobacter platensis WP_018962527.1' --------MRPVKTLEDLQKIREEASRKVNVRS-DRTG--IRITVGMATCGIAAGARPVMMAILDELEKRNVKG-VTVVETGCIGLCKYEPIVEVYEPDQDKVTYIKMDPEKARQVVVEHVINGHPIKEWTLESADIQ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 649; END; BEGIN NOTES; TAXABITS TAXA = Taxa NAME = newlyAddedTaxon on = 1 - 13; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 649; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 649; END; BEGIN TREES; Title 'Trees from "hydD.tre"'; LINK Taxa = Taxa; TRANSLATE [0] n0 'Caldanaerobacter subterraneus pacificus_CDSM653_0931', [1] n1 'Caldanaerobacter subterraneus yonseiensis_ERM93008.1', [2] n2 'Caldanaerobacter subterraneus tengcongensis_NP_622544.1', [3] n3 'Thermoanaerobacter sp. YP_001663748.1', [4] n4 'Thermoanaerobacter wiegelii YP_004819691.1', [5] n5 'Thermoanaerobacter italicus YP_003476668.1', [6] n6 'Thermoanaerobacter pseudethanolicus YP_001665444.1', [7] n7 'Thermoanaerobacterium thermosaccharolyticum YP_007298419.1', [8] n8 'Thermoanaerobacterium xylanolyticum YP_004471285.1', [9] n9 'Thermoanaerobacterium saccharolyticum YP_006392731.1', [10] n10 'Thermoanaerobacterium thermosaccharolyticum YP_003851722.1', [11] n11 'Coprothermobacter proteolyticus YP_002246549.1', [12] n12 'Coprothermobacter platensis WP_018962527.1'; TREE tree_1 = ((n12:0.093223,n11:0.000198)0.9890:0.182501,(((n10:0.000001,n7:0.00961)0.9020:0.019309,(n9:0.000001,n8:0.000001)0.0000:0.000001)0.9550:0.11834,(((n3:0.000001,(n2:0.000001,(n1:0.000001,n0:0.000001)0.0000:0.000001)0.9740:0.039957)0.8280:0.009623,(n4:0.000001,n6:0.009852)0.0000:0.000001)0.7590:0.009043,n5:0.010305)0.7310:0.038495)0.0180:0.053001)root; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1440596650343; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8475702303775682551; tell It; setDefaultOrder 9 8 7 6 10 12 11 3 5 4 2 1 0; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7439494739819176296; mqVersion 304; checksumv 0 3 253447428 null getNumChars 649 numChars 649 getNumTaxa 13 numTaxa 13 short false bits 1048575 states 1048575 sumSquaresStatesOnly 1.4983144036865E13 sumSquares 1.4983144036865E13 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 234; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 710 603; setLocation 51 24; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8475702303775682551 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8475702303775682551; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 476 531; setLocation 51 24; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; setActive; 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.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #7439494739819176296 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 476 531; setLocation 51 24; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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; toggleShowPaleExcluded 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 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;