#NEXUS [written Fri Apr 13 11:12:53 CEST 2018 by Mesquite version 3.40 (build 877) at PC-BORCHIELLINI/172.20.36.92] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=17; TAXLABELS M.musculus B.floridae D.melanogaster 'A.digitifera-1' M.leidyi T.adhaerens S.ciliatum S.coactum L.complicata O.lobularis 'Oscarella-sp' O.carmela 'A.digitifera-2' A.queenslandica P.ficiformis A.vestus O.minuta ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=250; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX M.musculus SNWR-QPELPEVIAML-GFRLDAVKSNAAAYLQHLCYRNDKVKTDVRKLKGIPILVGLLDHPKK-EVHLGACGALKNISFGR-DQDNKIAIKNCDGVPALVRLLRKARDMDLTEVITGTLWNLSSHDSIKMEIVDHALHALTDEVIIPHSGWERE----PNEDCKP-RHIEWESVLTNTAGCLRNVSSERS-EARRKLRECDGLVDALIFIVQAEIGQKDSDSKLVENCVCL----LRNLSYQVHREIP- B.floridae MAWR-DPDLPELIEML-REPHPPVQANAAAYLQHLCYGDDPVKAKIRSLGGIPELVQLLDHPSP-DVHRNAAGALRNLAYGKANDENKSAINNANGIPALVRLLRKTPDTEVQELVTGVLWNLSSHPPLKQAVIDDALTVLTNRIIIPHSGWEAS----PDADSKP-RDIQWSVVFRNATGCLRNVSSAGP-DARRKMRECDGLVDALLHVLQTAIGKNDMDNKSVENCQYMVPTELTNLKFVMTSSNC- D.melanogaster MRWR-DPNLSEVISFL-SNPSSAIKANAAAYLQHLCYMDDPNKQRTRSLGGIPPLVRLLSYDSP-EIHKNACGALRNLSYGRQNDENKRGIKNAGGIAALVHLLCRSQETEVKELVTGVLWNMSSCEDLKRSIIDEALVAVVCSVIKPHSGWDAV----------CCGETCFSTVFRNASGVLRNVSSAGE-HARGCLRNCEHLVECLLYVVRTSIEKNNIGNKTVENCVCI----LRNLSYRCQ-EVD- 'A.digitifera-1' TYAH-EPDLQDLLEYL-ESDDVTLIVNAANYLQHLSFSDDQVKIKVRGLGGIAILVRLLDHELE-EVHRSAAACLRNLSFSKARDENKLAIAECFGIEALIRLLKRTRKDEVKEVVLGVLWNLSSCEDLKLRIIEVCLIVLITIIIVPYSGWTKT----AAQSNAPIPSIKWSTVFRNASGVLRNVSSAGP-EARRVMRDCDGLVDSFVWIIKAPIGKNDIDNKSVENSICI----LRNLSYRLENEVD- M.leidyi TTSS-EPELQDIIKILTGSSNLSLVNTAAGALQHLSYGDDHMKNKIREAGAIPILVHMLSLDD--LVCISSLGVLRNLSFGKSNHLNRIAIQDAHGITLLVQLLNTTESFEIQELVTGVFWNLSSSDTLKLPILKQALESLVKNIIIPLSGWQETKSI-PFDQNGYNANISWTTVFRNATGCLKNLSSAGL-EGRTLLRLCHGLVDSLLWTVRCAQGKNDVDNKAVENAVCI----LRNLSYRLEAEVA- T.adhaerens SQKY-SLTIEDAVNML-KSDNSIHSINAAVHLQHACFNNDGVKATIKRLGGILHLVRMVDSKNE-EIQLSAIATLRNLAYGKANDESKGAILRHKGIPVLANVLRRTGSPHVREEIVRLLWNLSTLEAAKEQLLNLTLDVLAK-LIEDHS---------ISAGEGSLSDTQWPTIYANATGTLRNLSSSTNLSSRQMMRKLDHLINALITVTHLSVQRKDFDGKCVENSVCI----LRNLSYNLEEEVD- S.ciliatum SPAH-QLSLHDVVGFL-NSRDTMVVANAAGYLQHASYNNDHVKTQLRDLGAIPALVGLILQRDE-MVQHAAVGVLRNMSYGPHSVPNKYAVCEAGGVEVLVRLLRNARSEDVQELVTGVLWNLSSCEELKKHILSQSTTELVRSVIVPASGWDPSGDEDNEDNNDVLAQILWTSVLRNATGILRNLSSAGP-DARDVLRSTEGLVDALLRMLRAAVGNNEVDNKSVENSMCV----LRNLSFRMETEVD- S.coactum SPAH-QLSLHDVVGFL-NSRDTMVVANAAGYLQHASYNNDHVKAQLRDLGAIPVLVGLILQRDE-MVQHAAVGVLRNMSYGPRSVPNKYAVCEAGGVEVLVRLLRNARSEDVQELVTGVLWNLSSCEELKKHILTQGTTELVRSVIVPASGWDPSGDEDNEDNNDVLARIGWTSVLRNATGILRNLSSAGP-EARDVLRSTEGLVDALLRMLRAAVGNNEVDNKSVENSMCV----LRNLSFRMESEVD- L.complicata GPTH-QLSLGDVIGFL-NSRDTMVVANAAGYLQHASYNNDHVKSQLRDLGAIPVLVGLILQRDE-MVQHAAVGVLRNISYGSRSMPNKYSICENGGVEVLVRLLRNARSEDVQELVTGVLWNLSSCEELKMHILSQSTTELVRTVIVPASGWDPAGD-DTADSSEPMQRIGWTPVLRNATGILRNLSSAGP-SARELLRSTEGLADALLRMLRAAAGNNEVDNKSVENSMCV----LRNLSFRMESEVD- O.lobularis KQEQ-ELDLPEIIDLL-ASDDYLKVTNAAGLLQHMSYKDDEMKSQIKNEGAIPVLIDLLGSRHM-EVCHAVAGVLRNLCYGSTNNENKLAVRDAGGITALVHLLKTTRSIEVKELVCSVLWNISSFEGLKEDLLQESLHVLTHYVIRPESGIQAS----FQLTSRVAGELNNTLLLRNATGVFRNLSSASE-NARKAMRISPGLVDALFFIILSAENTPDVDSKTVENCVCI----LRNLSFRLENEVT- 'Oscarella-sp' ------MDLLEIIDLL-NSDDYQRVTHAAGLLQHLSYKDDDMKARIKNEGAIPVLIDLLGSRHV-EVCHAVAGVLRNLCYGSTNNENKLAVRDAGGINALVHLLKTTRSIEVKELVCSVLWNISSFEGLKEDLLRESLHVLTHYVIRPESGIQPS----FQLTSRVAGELNNTLLLRNATGVFRNLSSASE-NARKAMRISPGLVDALFFVILSAENTPDVDSKTVENCVCI----LRNLSFRLENEVP- O.carmela KEDE-NMDLPEIIDML-GSDDYRKVTHAAGLLQHLSYKDDMMKARIKSEGTIPVLIDLLGSRHV-EVCHAVAGVLRNLCYGSSNNENKLAVRDAGGITALVHLLKTTRSIEVKELVCSVLWNISSFDGLKEDLLRESLHVLTHYVIRPESGIQPS----FQLTSRVAGELNNTLLLRNATGVFRNLSSASD-NARKSMRISPGLVDALFFVILSAENTPDVDSKTVENCICI----LRNLSFRLEIEVS- 'A.digitifera-2' LVGQ-EPEIPDLIDYM-QSGDDVKVINAARYLQHLCFSKESVKDKVRELGGVPVIVRLLRHSEW-RVRYAAICLLRNLSFSMKYDANRLAIADCGGIEALIEILQQTNTIEHKEAILGVLCNLSSVQSLRLRILLVCLHIIVVVIIVPYSEWTAV----AARSQLPKREHPWPMVLVHATRLVRNLSSAGT-RARQELREEKDLVDCLVWIIRVGVKSGQFDDRCLEHSVCT----LRNLSYRLESEID- A.queenslandica HGSQHEPNLNDVVDYL-SHSDPSTVANAASYIQHLAYGDDNMKAKIRQFGGIPALLSQVRNPDP-RVQLAVLGALRNLSYGRANNESKSQIAQDAGLPNIVYLLRNNSQPEVRELVTSVLWNLSSCEDIKLRILQCSLKDIVDTILIPSTGYGPTYPA-ARDFSQRTSVLHWTAEMKNSLGAIRNISSAGV-EARRFLRASNNLVDTLVWIVRAAATQENVDEKTVENAICI----LRNLSFQIEDEVD- P.ficiformis TNTR-EPNLNDVVDFL-SSSDPTHVANAASYLQHLAYSDDNMKAKIRQFGGIPALISQLRTHDDIRVQVPVLGALRNLSYGRANIGNKIQIANDAGLTEMTLLLKTTQHSEIRELVTSVLWNLSSCEEIKLRIIHVCLKDVVEHILIPHSGYSHTHLA-AKDFSVRPDVTHWSPEMRNILGALRNISSAGE-EARRFLRSCNGLVDCLVWIIRAATGQENTDEKTAESAMCI----LRNLSYQLEDEVD- A.vestus TLSPTEAKAQELVRLIVTSQDLTTLCRSATIIQQMTYGDDVNKNYFREVGAIQALISHLQSRQD-SMLSCVLGALRNLSYGV--EFNKRIIASGWGLSNLMQLLMRTQFPELRELTTSVLWNASSSEYVKRAFLDVCVDDLVRSSVIPLANWDTESIPLNAMNPLNPSHVKWNAELKNSTGVLRNLASFGK-DCRRRLRRSVGLVDSVLYIVCSALGRDDLDNQIVENCLCI----LRNLSYRLEVEVD- O.minuta TLSPTEAKAQELVRILVTSQDITSLCRAATLIQQMTYGDDVVKAYFREVGAIQALISHLQSRQD-SVLSSSLGALRNLSYGV--ELNKRVIASGWGLSNLMQLLLRTQLPELRELTTGVLWNVSSSEYLKRGFLDICIDDLVRSSVIPLANWNTESVPLSAMDPSILSHVKWNAELKNSTGVLRNLTSFGK-ECRRRLRGCVGLVDSVLYIICSALGREDLDNQIVENCLCI----LRNLSYRMESEVD- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 250; END; BEGIN NOTES; TAXABITS NAME = newlyAddedTaxon on = 1 - 17; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 250; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 250; END; BEGIN TREES[!'Parameters: Tree search criterion: minimize Tree value using character matrix']; Title 'Trees from Mesquite''s heuristic search'; ID 0162be46b44116; LINK Taxa = Taxa; TRANSLATE [0] 1 M.musculus, [1] 2 B.floridae, [2] 3 D.melanogaster, [3] 4 'A.digitifera-1', [4] 5 M.leidyi, [5] 6 T.adhaerens, [6] 7 S.ciliatum, [7] 8 S.coactum, [8] 9 L.complicata, [9] 10 O.lobularis, [10] 11 'Oscarella-sp', [11] 12 O.carmela, [12] 13 'A.digitifera-2', [13] 14 A.queenslandica, [14] 15 P.ficiformis, [15] 16 A.vestus, [16] 17 O.minuta; TREE 'Tree 1 from search (criterion: minimize Tree value using character matrix)' = ((((4,(6,13)),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))),(1,2)),3)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 2 from search (criterion: minimize Tree value using character matrix)' = (((1,2),3),((4,(6,13)),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 3 from search (criterion: minimize Tree value using character matrix)' = ((1,2),(((4,(6,13)),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))),3))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 4 from search (criterion: minimize Tree value using character matrix)' = (((4,(6,13)),((1,2),3)),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5)))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 5 from search (criterion: minimize Tree value using character matrix)' = ((4,(6,13)),(((1,2),3),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 6 from search (criterion: minimize Tree value using character matrix)' = ((2,(((4,(6,13)),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))),3)),1)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 7 from search (criterion: minimize Tree value using character matrix)' = (2,(1,(((4,(6,13)),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))),3)))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 8 from search (criterion: minimize Tree value using character matrix)' = (((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),(((14,15),(17,16)),5))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 9 from search (criterion: minimize Tree value using character matrix)' = ((((11,12),10),(9,(8,7))),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5)))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 10 from search (criterion: minimize Tree value using character matrix)' = (((6,13),(((1,2),3),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5)))),4)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 11 from search (criterion: minimize Tree value using character matrix)' = ((6,13),(4,(((1,2),3),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5)))))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 12 from search (criterion: minimize Tree value using character matrix)' = ((((14,15),(17,16)),((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3)))),5)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 13 from search (criterion: minimize Tree value using character matrix)' = (((14,15),(17,16)),(((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),5))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 14 from search (criterion: minimize Tree value using character matrix)' = (((9,(8,7)),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5))),((11,12),10))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 15 from search (criterion: minimize Tree value using character matrix)' = ((9,(8,7)),(((11,12),10),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5))))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 16 from search (criterion: minimize Tree value using character matrix)' = ((13,(4,(((1,2),3),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))))),6)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 17 from search (criterion: minimize Tree value using character matrix)' = (13,(6,(4,(((1,2),3),((((11,12),10),(9,(8,7))),(((14,15),(17,16)),5))))))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 18 from search (criterion: minimize Tree value using character matrix)' = (((17,16),(((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),5)),(14,15))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 19 from search (criterion: minimize Tree value using character matrix)' = ((17,16),((14,15),(((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),5)))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 20 from search (criterion: minimize Tree value using character matrix)' = (((11,12),((9,(8,7)),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5)))),10)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 21 from search (criterion: minimize Tree value using character matrix)' = ((11,12),(((9,(8,7)),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5))),10))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 22 from search (criterion: minimize Tree value using character matrix)' = (((8,7),(((11,12),10),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5)))),9)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 23 from search (criterion: minimize Tree value using character matrix)' = ((8,7),(9,(((11,12),10),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5)))))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 24 from search (criterion: minimize Tree value using character matrix)' = ((14,((17,16),(((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),5))),15)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 25 from search (criterion: minimize Tree value using character matrix)' = (14,(((17,16),(((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),5)),15))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 26 from search (criterion: minimize Tree value using character matrix)' = ((16,((14,15),(((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),5))),17)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 27 from search (criterion: minimize Tree value using character matrix)' = (16,(17,((14,15),(((((11,12),10),(9,(8,7))),((4,(6,13)),((1,2),3))),5))))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 28 from search (criterion: minimize Tree value using character matrix)' = ((12,(((9,(8,7)),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5))),10)),11)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 29 from search (criterion: minimize Tree value using character matrix)' = (12,(11,(((9,(8,7)),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5))),10)))[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 30 from search (criterion: minimize Tree value using character matrix)' = ((7,(9,(((11,12),10),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5))))),8)[% ] [% ] [% setBetweenBits = selected ]; TREE 'Tree 31 from search (criterion: minimize Tree value using character matrix)' = (7,(8,(9,(((11,12),10),(((4,(6,13)),((1,2),3)),(((14,15),(17,16)),5))))))[% ] [% ] [% setBetweenBits = selected ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1523610773691; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8549115390609765854; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 820215273920938208; mqVersion 340; checksumv 0 3 2008380529 null getNumChars 250 numChars 250 getNumTaxa 17 numTaxa 17 short false bits 1048575 states 1048575 sumSquaresStatesOnly 3.2436088389524E13 sumSquares 3.2436088389524E13 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 201; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8549115390609765854 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 0162be46b44116; toggleUseWeights off; endTell; setAssignedID 2259.1523610752440.2703599229995604318; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 499 392; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; 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 off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; 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; toggleShow consensusFrequency; toggleShow bootstrapFrequency; toggleShow posteriorProbability; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; toggleShowOnTerminals on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;