#NEXUS [written Sat Jun 07 11:48:06 PDT 2008 by Mesquite version 2.5 BETA 2 (build j76) at Thrandina.local/192.168.0.136 (Wayne Maddison)] BEGIN TAXA; TITLE Untitled_Block_of_Taxa; DIMENSIONS NTAX=140; TAXLABELS taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32 taxon_33 taxon_34 taxon_35 taxon_36 taxon_37 taxon_38 taxon_39 taxon_40 taxon_41 taxon_42 taxon_43 taxon_44 taxon_45 taxon_46 taxon_47 taxon_48 taxon_49 taxon_50 taxon_51 taxon_52 taxon_53 taxon_54 taxon_55 taxon_56 taxon_57 taxon_58 taxon_59 taxon_60 taxon_61 taxon_62 taxon_63 taxon_64 taxon_65 taxon_66 taxon_67 taxon_68 taxon_69 taxon_70 taxon_71 taxon_72 taxon_73 taxon_74 taxon_75 taxon_76 taxon_77 taxon_78 taxon_79 taxon_80 taxon_81 taxon_82 taxon_83 taxon_84 taxon_85 taxon_86 taxon_87 taxon_88 taxon_89 taxon_90 taxon_91 taxon_92 taxon_93 taxon_94 taxon_95 taxon_96 taxon_97 taxon_98 taxon_99 taxon_100 taxon_101 taxon_102 taxon_103 taxon_104 taxon_105 taxon_106 taxon_107 taxon_108 taxon_109 taxon_110 taxon_111 taxon_112 taxon_113 taxon_114 taxon_115 taxon_116 taxon_117 taxon_118 taxon_119 taxon_120 taxon_121 taxon_122 taxon_123 taxon_124 taxon_125 taxon_126 taxon_127 taxon_128 taxon_129 taxon_130 taxon_131 taxon_132 taxon_133 taxon_134 taxon_135 taxon_136 taxon_137 taxon_138 taxon_139 taxon_140 ; IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 WM114911cd1be833 WM114911cd1be834 WM114911cd1be835 WM114911cd1be836 WM114911cd1be837 WM114911cd1bf838 WM114911cd1bf839 WM114911cd1bf840 WM114911cd1bf841 WM114911cd1bf842 WM114911cd1bf843 WM114911cd1bf844 WM114911cd1bf845 WM114911cd1bf846 WM114911cd1bf847 WM114911cd1bf848 WM114911cd1c0849 WM114911cd1c0850 WM114911cd1c0851 WM114911cd1c0852 WM114911cd1c2853 WM114911cd1c2854 WM114911cd1c2855 WM114911cd1c3856 WM114911cd1c3857 WM114911cd1c3858 WM114911cd1c3859 WM114911cd1c3860 WM114911cd1c3861 WM114911cd1c3862 WM114911cd1c3863 WM114911cd1c5864 WM114911cd1c6865 WM114911cd1c6866 WM114911cd1c7867 WM114911cd1c7868 WM114911cd1c7869 WM114911cd1c7870 WM114911cd1c7871 WM114911cd1c7872 WM114911cd1c7873 WM114911cd1c7874 WM114911cd1c7875 WM114911cd1c7876 WM114911cd1c7877 WM114911cd1c7878 WM114911cd1c7879 WM114911cd1c7880 WM114911cd1c7881 WM114911cd1c7882 WM114911cd1c8883 WM114911cd1c8884 WM114911cd1c8885 WM114911cd1c8886 WM114911cd1c8887 WM114911cd1c8888 WM114911cd1c8889 WM114911cd1c8890 WM114911cd1c8891 WM114911cd1c8892 WM114911cd1c8893 WM114911cd1c8894 WM114911cd1c8895 WM114911cd1c8896 WM114911cd1c8897 WM114911cd1c9898 WM114911cd1c9899 WM114911cd1c9900 WM11493f556ad233 WM11493f556ad234 WM11493f556ad235 WM11493f556ad236 WM11493f556ad237 WM11493f556ad238 WM11493f556ad239 WM11493f556ad240 WM11493f556ad241 WM11493f556ad242 WM11493f556ad243 WM11493f556ae244 WM11493f556ae245 WM11493f556ae246 WM11493f556ae247 WM11493f556ae248 WM11493f556ae249 WM11493f556ae250 WM11493f556ae251 WM11493f556ae252 WM11493f556af253 WM11493f556af254 WM11493f556af255 WM11493f556af256 WM11493f556af257 WM11493f556af258 WM11493f556af259 WM11493f556af260 WM11493f556af261 WM11493f556af262 WM11493f556af263 WM11493f556af264 WM11493f556af265 WM11493f556af266 WM11493f556af267 WM11493f556af268 WM11493f556af269 WM11493f556af270 WM11493f556af271 WM11493f556af272 ; BLOCKID WM1148f47d2081; END; BEGIN CHARACTERS; TITLE 'Matrix in file "08-binaryTreeSim.nex"'; DIMENSIONS NCHAR=5; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1"; CHARSTATELABELS 1 Sim._with_tree_1, 2 Sim._with_tree_2, 3 Sim._with_tree_3, 4 Sim._with_tree_4, 5 Sim._with_tree_5 ; MATRIX taxon_1 11001 taxon_2 11111 taxon_3 11111 taxon_4 01111 taxon_5 11111 taxon_6 11111 taxon_7 11111 taxon_8 11111 taxon_9 11011 taxon_10 01111 taxon_11 11111 taxon_12 11111 taxon_13 11111 taxon_14 11111 taxon_15 11111 taxon_16 11101 taxon_17 11111 taxon_18 11111 taxon_19 11111 taxon_20 11111 taxon_21 11111 taxon_22 11111 taxon_23 11111 taxon_24 11111 taxon_25 11111 taxon_26 11111 taxon_27 11111 taxon_28 11111 taxon_29 11111 taxon_30 11111 taxon_31 11111 taxon_32 11111 taxon_33 11111 taxon_34 11111 taxon_35 11111 taxon_36 11111 taxon_37 11111 taxon_38 11111 taxon_39 11111 taxon_40 11111 taxon_41 11111 taxon_42 01111 taxon_43 11111 taxon_44 11111 taxon_45 11111 taxon_46 11111 taxon_47 11111 taxon_48 11111 taxon_49 11111 taxon_50 01111 taxon_51 11111 taxon_52 11111 taxon_53 11111 taxon_54 11111 taxon_55 11111 taxon_56 11111 taxon_57 01111 taxon_58 11111 taxon_59 11111 taxon_60 11111 taxon_61 11111 taxon_62 11111 taxon_63 11111 taxon_64 11111 taxon_65 11111 taxon_66 11111 taxon_67 11111 taxon_68 11111 taxon_69 11111 taxon_70 11111 taxon_71 11111 taxon_72 01111 taxon_73 11111 taxon_74 11111 taxon_75 11111 taxon_76 11111 taxon_77 11111 taxon_78 11111 taxon_79 11111 taxon_80 11111 taxon_81 11111 taxon_82 11111 taxon_83 11111 taxon_84 11111 taxon_85 11111 taxon_86 11111 taxon_87 11111 taxon_88 11111 taxon_89 11011 taxon_90 11111 taxon_91 11111 taxon_92 11111 taxon_93 11111 taxon_94 11111 taxon_95 11111 taxon_96 11111 taxon_97 11111 taxon_98 11111 taxon_99 11111 taxon_100 11111 taxon_101 ????? taxon_102 ????? taxon_103 ????? taxon_104 ????? taxon_105 ????? taxon_106 ????? taxon_107 ????? taxon_108 ????? taxon_109 ????? taxon_110 ????? taxon_111 ????? taxon_112 ????? taxon_113 ????? taxon_114 ????? taxon_115 ????? taxon_116 ????? taxon_117 ????? taxon_118 ????? taxon_119 ????? taxon_120 ????? taxon_121 ????? taxon_122 ????? taxon_123 ????? taxon_124 ????? taxon_125 ????? taxon_126 ????? taxon_127 ????? taxon_128 ????? taxon_129 ????? taxon_130 ????? taxon_131 ????? taxon_132 ????? taxon_133 ????? taxon_134 ????? taxon_135 ????? taxon_136 ????? taxon_137 ????? taxon_138 ????? taxon_139 ????? taxon_140 ????? ; IDS WM11493f556a312 WM11493f556a313 WM11493f556a314 WM11493f556a315 WM11493f556a316 ; BLOCKID WM1149667c69b0; END; BEGIN TREES; Title 'Trees from "08-binaryTreeSim.nex"'; LINK Taxa = Untitled_Block_of_Taxa; TRANSLATE 1 taxon_1, 2 taxon_2, 3 taxon_3, 4 taxon_4, 5 taxon_5, 6 taxon_6, 7 taxon_7, 8 taxon_8, 9 taxon_9, 10 taxon_10, 11 taxon_11, 12 taxon_12, 13 taxon_13, 14 taxon_14, 15 taxon_15, 16 taxon_16, 17 taxon_17, 18 taxon_18, 19 taxon_19, 20 taxon_20, 21 taxon_21, 22 taxon_22, 23 taxon_23, 24 taxon_24, 25 taxon_25, 26 taxon_26, 27 taxon_27, 28 taxon_28, 29 taxon_29, 30 taxon_30, 31 taxon_31, 32 taxon_32, 33 taxon_33, 34 taxon_34, 35 taxon_35, 36 taxon_36, 37 taxon_37, 38 taxon_38, 39 taxon_39, 40 taxon_40, 41 taxon_41, 42 taxon_42, 43 taxon_43, 44 taxon_44, 45 taxon_45, 46 taxon_46, 47 taxon_47, 48 taxon_48, 49 taxon_49, 50 taxon_50, 51 taxon_51, 52 taxon_52, 53 taxon_53, 54 taxon_54, 55 taxon_55, 56 taxon_56, 57 taxon_57, 58 taxon_58, 59 taxon_59, 60 taxon_60, 61 taxon_61, 62 taxon_62, 63 taxon_63, 64 taxon_64, 65 taxon_65, 66 taxon_66, 67 taxon_67, 68 taxon_68, 69 taxon_69, 70 taxon_70, 71 taxon_71, 72 taxon_72, 73 taxon_73, 74 taxon_74, 75 taxon_75, 76 taxon_76, 77 taxon_77, 78 taxon_78, 79 taxon_79, 80 taxon_80, 81 taxon_81, 82 taxon_82, 83 taxon_83, 84 taxon_84, 85 taxon_85, 86 taxon_86, 87 taxon_87, 88 taxon_88, 89 taxon_89, 90 taxon_90, 91 taxon_91, 92 taxon_92, 93 taxon_93, 94 taxon_94, 95 taxon_95, 96 taxon_96, 97 taxon_97, 98 taxon_98, 99 taxon_99, 100 taxon_100, 101 taxon_101, 102 taxon_102, 103 taxon_103, 104 taxon_104, 105 taxon_105, 106 taxon_106, 107 taxon_107, 108 taxon_108, 109 taxon_109, 110 taxon_110, 111 taxon_111, 112 taxon_112, 113 taxon_113, 114 taxon_114, 115 taxon_115, 116 taxon_116, 117 taxon_117, 118 taxon_118, 119 taxon_119, 120 taxon_120, 121 taxon_121, 122 taxon_122, 123 taxon_123, 124 taxon_124, 125 taxon_125, 126 taxon_126, 127 taxon_127, 128 taxon_128, 129 taxon_129, 130 taxon_130, 131 taxon_131, 132 taxon_132, 133 taxon_133, 134 taxon_134, 135 taxon_135, 136 taxon_136, 137 taxon_137, 138 taxon_138, 139 taxon_139, 140 taxon_140; TREE 'Simulated Tree (with character) 1' = (((13:0.26414291654120825,89:0.26414291654120825):12.66569902022103,((4:2.245005924397304,(57:1.4365952502271064,72:1.4365952502271064):0.808410674170198):10.061848574720196,((((5:6.7062377792435,(21:4.397116509475041,(((33:1.493667627615986,71:1.493667627615986):2.5854357019863663,((40:2.976067881831738,53:2.976067881831738):0.2557339990166187,49:3.2318018808483564):0.8473014487539956):0.09137888232724879,(36:3.179102152041311,50:3.179102152041311):0.9913800598882901):0.22663429754544118):2.3091212697684607):3.518503950551628,((9:1.5186424029407128,79:1.5186424029407128):5.425043693114888,(((20:0.060872138035395054,100:0.060872138035395054):0.5396378740179559,70:0.600510012053351):3.8277264848078665,((32:0.17351680614352843,95:0.17351680614352843):2.1210541079926495,56:2.294570914136178):2.1336655827250377):2.515449599194386):3.2810556337395282):0.3969769610145193,(((7:5.880348131901751,((24:1.8461274545522233,61:1.8461274545522233):2.214104827610751,(41:3.8204822999218067,((44:3.734250582554956,(47:1.205241591143171,74:1.205241591143171):2.5290089914117844):0.023951544392953317,((((46:0.6267857993488887,84:0.6267857993488887):1.2834109408488483,59:1.9101967401977367):1.0987465244014505,((52:0.5692481011945624,86:0.5692481011945624):1.9014370957499651,(38:1.0694777667754722,80:1.0694777667754722):1.4012074301690551):0.5382580676546599):0.07561090075659263,51:3.0845541653557804):0.6736479615921294):0.06228017297389717):0.23974998224116803):1.8201158497387784):4.134310575204565,10:10.014658707106321):0.4901431194171596,(((8:4.163113541861947,(37:0.18253278397313646,94:0.18253278397313646):3.980580757888812):4.159507759429159,(((((19:0.9766218603579516,30:0.9766218603579516):1.5788503277994184,(11:1.608322096260005,67:1.608322096260005):0.9471500918973647):0.27726495199177836,(43:1.7785445146679395,(62:0.588890406554164,85:0.588890406554164):1.1896541081137755):1.0541926254812082):2.9200186443184437,(91:1.162257290837547,(78:0.009932620523370156,25:0.009932620523370156):1.152324670314177):4.590498493630045):0.9064312372237074,((22:0.21498506318373276,90:0.21498506318373276):4.070510144387209,((35:0.23933231356153234,58:0.23933231356153234):3.5536050757442554,(45:2.1288396210862595,(31:1.6606616092574882,(65:1.0393561923200985,(12:0.767544560493447,82:0.767544560493447):0.2718116318266515):0.6213054169373896):0.4681780118287714):1.6640977682195275):0.4925578182651544):2.3736918141203582):1.6634342795998078):0.8599725619460677,(14:1.7667036679456574,((((63:0.07686913089463243,99:0.07686913089463243):0.1258923576742496,92:0.20276148856888204):0.3174257291361061,(87:0.09050884369455534,98:0.09050884369455534):0.4296783740104329):1.018320912620936,69:1.538508130325924):0.22819553761973335):7.415890195291518):1.3222079632863026):0.11691686428617315):0.8408299919959468,((2:0.1284228692947272,97:0.1284228692947272):6.953479919103079,(((16:1.6297182589547838,(66:0.6703132478395832,(83:0.1935835927363961,93:0.1935835927363961):0.4767296551031871):0.9594050111152007):3.9719905758855343,55:5.601708834840316):0.5176123565014688,(((23:1.365062522573327,73:1.365062522573327):1.3645171617630303,54:2.729579684336358):2.533970968657945,(15:4.330233104248458,(34:4.145950900901953,39:4.145950900901953):0.18428220334650336):0.9333175487458454):0.8557705383474827):0.9625815970560223):4.380645894407789):0.8443058163119082):0.6229874376447343):7.059791104447394,(((3:8.513740229195653,(17:4.739455570899427,(48:1.8712991556213066,((60:1.3061966303196677,26:1.3061966303196677):0.35901653415762047,(64:1.1840144821443028,76:1.1840144821443028):0.48119868233298524):0.2060859911440184):2.868156415278121):3.774284658296225):1.1525210363913716,((18:1.5554082816811872,68:1.5554082816811872):0.6268304875655505,6:2.1822387692467378):7.4840224963402875):1.587873487646932,(((27:0.37401140727614246,88:0.37401140727614246):0.823965651150295,75:1.1979770584264373):3.979653264512042,(((28:0.939022817722179,81:0.939022817722179):1.0658124432901779,77:2.0048352610123565):3.135367262896273,(((29:0.16429534179711944,96:0.16429534179711944):2.2548813340345593,42:2.419176675831679):0.4432035607309688,1:2.862380236562648):2.2778222873459812):0.03742779902984921):6.0765044302954765):8.735498287975677):3.7256163307418646; TREE 'Simulated Tree (with character) 2' = ((((57:8.740564889482517,12:8.740564889482515):0.08951737253490406,(11:2.686632950623149,49:2.6866329506231486):6.143449311394269):1.9682270009255305,3:10.798309262942945):0.10691079279564765,((((((((((2:0.3076379941221983,94:0.3076379941221983):0.14765376902865543,(87:0.008091472062248412,100:0.008091472062248412):0.44720029108860526):1.1528414010681944,(62:1.5798099269923387,80:1.5798099269923387):0.028323237226710315):5.315645902764501,(13:5.427483239484042,(((20:3.11650308421794,(41:0.9158831495464465,79:0.9158831495464465):2.200619934671493):0.5344693429164447,(((98:0.42756004582895846,(89:0.36854419995258514,91:0.36854419995258514):0.059015845876373325):0.14889341215792307,1:0.5764534579868814):1.5761993216099102,(55:0.807861401466335,(33:0.3350143090634801,93:0.3350143090634801):0.47284709240285483):1.344791378130457):1.4983196475375926):0.4815375829041647,(28:3.9941038884984903,(30:2.4181038195218245,((52:0.4246360043050929,90:0.4246360043050929):0.25043353606568736,82:0.6750695403707802):1.7430342791510443):1.5760000689766653):0.1384061215400595):1.2949732294454952):1.4962958274995035):1.4968179543745528,(15:5.2737616970440175,(22:0.5348296081543352,84:0.5348296081543352):4.738932088889688):3.1468353243140794):0.002781620347024277,((14:2.7322253826722878,((46:1.6668970729162649,60:1.6668970729162649):0.6935904741436052,(53:1.6132325562731247,61:1.6132325562731247):0.7472549907867456):0.37173783561241736):1.6988736555899044,26:4.4310990382621895):3.9922796034429324):0.8484723550667577,((9:1.0450328356424765,(75:0.973385256688017,76:0.973385256688017):0.07164757895445921):2.7469328222790916,((34:0.3590256678395345,92:0.3590256678395345):1.8910371842823481,(19:1.8242948345437477,58:1.8242948345437477):0.42576801757813487):1.5419028057996849):5.479885338850315):0.22232880504972338,((8:3.2856717760404406,(38:1.4743884463499073,68:1.4743884463499073):1.8112833296905335):3.237346843293854,(21:1.5008896601114354,(65:0.5617372265952054,((39:0.07784758777025433,50:0.07784758777025433):0.09932349078311506,97:0.1771710785533694):0.38456614804183625):0.9391524335162292):5.022128959222861):2.971161182487311):0.05708260340489333,((((7:5.48888373202122,(((((5:0.18420335846744368,96:0.18420335846744368):2.27149878149906,(((51:1.16969447288362,(73:0.028919896279563123,88:0.028919896279563123):1.140774576604057):0.01777056180200225,72:1.1874650346856221):0.613963916116492,59:1.8014289508021137):0.6542731891643906):1.2960278368496239,35:3.751729976816129):0.138588682078231,32:3.8903186588943597):1.5916737287553422,((17:1.6079383881174023,63:1.6079383881174023):1.2175320194587025,((44:0.4838182454508701,86:0.4838182454508701):0.9944012962239468,(67:1.295990157973416,(69:0.03557175281417003,31:0.03557175281417003):1.260418405159246):0.182229383701401):1.3472508659012876):2.656521980073596):0.006891344371521752):2.4634933257657496,((18:0.011149005001483784,99:0.011149005001483784):4.809055110269699,(((25:0.9217699427436866,78:0.9217699427436866):0.044261380638359285,(77:0.6604124169073572,83:0.6604124169073572):0.3056189064746885):1.7283250274407689,48:2.6943563508228148):2.1258477644483698):3.1321729425157874):0.3934006938868019,((16:2.5749700580008836,4:2.5749700580008836):1.421928872919795,(29:3.580806199672173,37:3.580806199672173):0.416092731248506):4.348878820753095):0.6479950937895768,((((10:1.2823903400314853,70:1.2823903400314853):1.6231805477694585,(43:2.7969217787282195,((45:0.6963351967892236,81:0.6963351967892236):2.013395468340936,(47:0.5452175941576847,(64:0.5257860276991528,85:0.5257860276991528):0.019431566458531876):2.164513070972475):0.08719111359805985):0.10864910907272407):2.025536615762459,((24:2.1394585653285936,(56:0.22496381768406132,95:0.22496381768406132):1.9144947476445322):1.699441536121825,(((27:0.12603545284833817,36:0.12603545284833817):1.1093486726156734,71:1.2353841254640117):0.06289407147322923,54:1.2982781969372412):2.540621904513178):1.092207402112983):0.008231301310871858,(23:3.1858716003759304,(40:1.0494313286292454,74:1.0494313286292454):2.1364402717466855):1.7534672044983433):4.054434040589077):0.5574895597631485):1.2283752595847288,((6:1.4922210838540175,66:1.4922210838540175):1.4477885910245092,42:2.9400096748785263):7.8396279899327):0.12558239092736778):0.0; TREE 'Simulated Tree (with character) 3' = (((((((1:1.5622844604031214,68:1.5622844604031214):0.6620126144845917,(56:1.0301802241163402,78:1.0301802241163402):1.1941168507713722):1.7548017644175342,(32:0.16290197669355147,99:0.16290197669355147):3.8161968626116964):2.4374614041472977,((15:0.6272692628633048,89:0.6272692628633048):3.036006628479801,(((38:0.48495012101992835,94:0.48495012101992835):0.5399002029330823,(79:0.906466918413682,((81:0.2517086324661378,96:0.2517086324661378):0.31916226785831986,92:0.5708709003244575):0.3355960180892244):0.11838340553932859):1.1766751384131762,57:2.2015254623661864):1.4617504289769185):2.753284352109439):0.04600923274586818,28:6.462569476198413):0.08525655306218673,(13:5.2098104278660715,(23:3.35111439112681,(43:2.4710429352475183,(54:0.8869993615929336,82:0.8869993615929336):1.5840435736545853):0.8800714558792901):1.858696036739262):1.3380156013945281):5.074459397616571,(((((((2:0.6361995821183353,87:0.6361995821183353):1.2419417962246266,(61:1.686160150897463,66:1.686160150897463):0.19198122744549945):3.2702579837434143,24:5.148399362086377):1.7776803502130931,(((10:1.0482540317882485,76:1.0482540317882485):0.892211853472459,60:1.940465885260707):1.776018150967579,(36:1.3798911778721075,70:1.3798911778721075):2.336592858356179):3.209595676071182):0.09004196284036342,(9:5.787207174552948,(20:1.984530179391105,59:1.984530179391105):3.802676995161842):1.2289145005868856):1.2113564489016861,(((5:4.2786516010476285,(31:0.3115934358085691,95:0.3115934358085691):3.9670581652390595):0.7989358374588416,(25:3.3635581805692,42:3.3635581805692):1.7140292579372702):0.6815549118614022,((21:0.2447669935952402,97:0.2447669935952402):3.3788032939775148,((39:1.634867116710081,67:1.634867116710081):1.498397336720212,47:3.133264453430293):0.49030583414246093):2.1355720627951182):2.4683357736736475):2.4588398198385644,(((((3:2.9994059296878453,46:2.9994059296878457):1.4371414832447278,(30:0.8594502198976846,83:0.8594502198976846):3.577097193034889):1.4395832940551563,(19:3.6692914131923056,(37:3.020494564315019,45:3.020494564315019):0.6487968488772861):2.2068392937954244):2.070972824950238,(((6:3.561329191409625,(22:1.0464547219346374,77:1.0464547219346374):2.5148744694749867):0.3018069694693989,33:3.863136160879023):0.6117015949998396,((29:2.685192451043383,(50:0.2427513964727859,98:0.2427513964727859):2.442441054570597):1.1483280857864022,((((34:0.8224932138298606,84:0.8224932138298606):0.508553945425676,73:1.331047159255537):2.0505830383231833,41:3.381630197578721):0.39005873966633253,(35:2.1094170588027414,58:2.1094170588027414):1.66227187844231):0.06183159958473338):0.6413172190490762):3.4722657760591056):0.47275748159137665,((((((4:1.801387476843813,64:1.801387476843813):0.06011584613510922,((62:1.0992550939226993,51:1.0992550939226993):0.35550612778633683,(69:0.6274942885752053,88:0.6274942885752053):0.8272669331338305):0.40674210126988636):0.782405045114069,52:2.643908368092991):1.0623953973279716,(14:3.4899670063329236,40:3.4899670063329236):0.21633675908804068):3.4342371477486258,((((((8:1.3771129980998764,72:1.3771129980998764):0.0022768035859159776,(71:0.5773029994229125,91:0.5773029994229125):0.8020868022628794):1.1525248496733167,53:2.5319146513591075):0.14312567157050152,(65:0.5073776286261943,49:0.5073776286261943):2.1676626943034165):3.34002870010037,(18:2.111281221641564,(26:1.2175662932245337,74:1.2175662932245337):0.893714928417031):3.903787801388416):0.6578694344478665,((((11:1.8027956834565582,63:1.8027956834565582):1.1913673995748777,48:2.9941630830314363):3.3726014421814083,(16:0.6071419533909189,90:0.6071419533909189):5.759622571821925):0.21290265274631434,12:6.579667177959158):0.09327127951868822):0.46760245569174275):0.08584632360500134,((7:2.4346036847290637,55:2.4346036847290637):3.7033582990394107,((17:2.294630160656669,44:2.294630160656669):2.403830289966331,(27:1.0535892893225007,(((75:0.5520898814559375,93:0.5520898814559375):0.23889442898561472,(85:0.0029591711662563442,100:0.0029591711662563442):0.788025139275296):0.15253330466041856,(80:0.784673817543995,86:0.784673817543995):0.15884379755797587):0.11007167422052976):3.6448711613005007):1.439501533145474):1.088425253006116):1.193473776754753):2.266456930350739):0.9359674829970878):3.5191706469292106; TREE 'Simulated Tree (with character) 4' = (1:15.208188673335862,((12:5.178290028326698,(5:4.979128402850933,28:4.979128402850933):0.19916162547576394):8.425939537084158,(((4:3.01780032402549,53:3.01780032402549):8.353066041129946,((((16:0.6015336970588279,90:0.6015336970588279):0.7258305059401745,71:1.3273642029990025):8.264151809784806,(10:3.323232475098665,((50:1.0205650056491342,(72:0.4423424282945011,92:0.4423424282945011):0.578222577354633):1.3985087173354256,(58:1.8742249257302126,(((66:0.7685420106983527,82:0.7685420106983527):0.06883998854642338,77:0.8373819992447761):0.3951388592437685,68:1.2325208584885448):0.6417040672416676):0.5448487972543473):0.9041587521141049):6.268283537685145):0.42834879670714177,(((19:2.152502562433341,61:2.152502562433341):3.767564446656531,((((41:0.18992268538928164,98:0.18992268538928164):4.393933218039402,(33:0.0906825897551103,99:0.0906825897551103):4.493173313673574):0.8038303172770894,(((((3:0.6716096754012838,86:0.6716096754012838):0.12065506449136351,81:0.7922647398926473):3.0936679805249043,(46:0.8208993020459833,80:0.8208993020459833):3.065033418371568):0.6885131185462651,((((35:1.0311041575993214,(45:1.0208425002240737,59:1.0208425002240737):0.010261657375247608):1.2630439907657007,60:2.2941481483650223):1.1913204389091103,((7:0.9677084367304624,75:0.9677084367304624):2.049727310133256,(54:2.057882964038904,63:2.0578829640389036):0.9595527828248144):0.468032840410414):0.5612051696066694,42:4.046673756880802):0.5277720820830151):0.5080185134836614,27:5.082464352447481):0.30522186825829406):0.22910486640859573,(26:1.482063037452363,70:1.482063037452363):4.134728049662005):0.3032759219755037):2.323565909068004,((14:0.36261987585358024,96:0.36261987585358024):7.181443856005232,((17:3.50085555087687,(48:0.6142593675218075,87:0.6142593675218075):2.886596183355062):3.9019791801511925,18:7.402834731028067):0.14122900083074552):0.6995691862990684):1.7762318913330764):1.3510015556644845):0.15602062478914008,(2:10.695719514410577,((((((((6:0.977071138574732,74:0.977071138574732):1.5528519510437722,(57:1.7887525264544595,24:1.7887525264544595):0.7411705631640448):1.7792767725520775,38:4.309199862170582):1.4566826077883408,((((((23:1.293491903935122,22:1.293491903935122):0.728672626032339,65:2.02216452996746):1.246407244826035,((51:0.15543910398304717,67:0.15543910398304717):0.19577377466463983,97:0.351212878647687):2.9173588961458083):1.4707002390055774,32:4.739272013799075):0.11381939205104151,((29:3.1557218969104603,((52:0.6731431511469523,85:0.6731431511469523):1.4696847636948525,(62:0.4254426761038135,94:0.4254426761038135):1.7173852387379915):1.0128939820686549):1.6552030814585157,(31:0.8220494901122285,79:0.8220494901122285):3.988875488256747):0.042166427481139385):0.8918073707471179,(49:4.815697044672432,((30:3.9208979104295754,(44:3.6975330298703772,37:3.6975330298703772):0.2233648805591985):0.6564579880673511,((34:0.6085962663970552,89:0.6085962663970552):1.1606165961062804,95:1.7692128625033356):2.808143035993592):0.23834114617550456):0.9292017319248016):0.02098369336168961):0.2576785208945612,(((20:0.9948855805393461,(73:0.8342221590758695,(78:0.0681754962417517,100:0.0681754962417517):0.7660466628341178):0.16066342146347645):3.2748921660122825,(40:0.7208649817850351,84:0.7208649817850351):3.5489127647665937):1.4388493080942721,(25:3.633660755158288,(47:0.43136277326609107,93:0.43136277326609107):3.2022979818921966):2.0749662994876137):0.3149339362075828):3.3652859200260123,(11:0.7634718081926234,(83:0.6131305786469455,88:0.6131305786469455):0.1503412295456777):8.62537510268687):0.680474412528486,(((8:0.6168202283654758,(9:0.3713533737761071,39:0.3713533737761071):0.2454668545893688):7.0413516656959,((15:0.9279831436974715,76:0.9279831436974715):3.5853205337387974,(((36:2.330186186709684,(69:2.0333989651724966,64:2.0333989651724966):0.2967872215371867):0.2519597200380178,(56:0.5475976102149023,91:0.5475976102149023):2.0345482965327992):0.0568137532565382,55:2.6389596600042395):1.8743440174320294):3.1448682166251043):0.9456521482094988,(13:6.0044264419414,21:6.004426441941402):2.5993976003294748):1.4654972811371096):0.008054492158297745,43:10.077375815566274):0.6183436988442993):0.831167475533998):2.077342575466275):1.6039591079250124):0.0; TREE 'Simulated Tree (with character) 5' = ((((((((26:0.23038280848456946,91:0.23038280848456946):0.1019006233978754,67:0.3322834318824449):0.8900761763597418,(68:0.42710801362424444,86:0.42710801362424444):0.7952515946179421):1.2332693329896927,((48:1.0315561945675082,74:1.0315561945675082):0.2834716738487835,41:1.315027868416292):1.1406010728155873):5.133045939225098,((13:6.274108818958306,(21:1.062440989315495,72:1.062440989315495):5.211667829642811):0.12429726790346002,(20:5.802789708215656,(24:3.4896033232532417,37:3.4896033232532417):2.313186384962418):0.595616378646109):1.1902687935952083):0.9708607904438425,(((((9:2.4695758147865554,(46:2.4437769979575084,(49:1.2211004721677334,69:1.2211004721677334):1.2226765257897745):0.025798816829047447):2.635458258748637,33:5.105034073535192):0.11308432730114414,((31:2.364293423602608,((51:0.017426369555112668,99:0.017426369555112668):1.0577782941996718,70:1.0752046637547843):1.289088759847823):0.05575832809025013,(50:2.1304414664510225,((54:0.2710657735789376,89:0.2710657735789376):0.5288196144801881,(77:0.07728327694030956,95:0.07728327694030956):0.7226021111188161):1.3305560783918957):0.2896102852418361):2.798066649143479):0.3810691740493959,((25:1.6243054962673933,(4:1.426854405468879,66:1.426854405468879):0.19745109079851392):0.24909680658603062,(57:0.3761130316116257,(87:0.0023281513310519078,100:0.0023281513310519078):0.3737848802805738):1.497289271241798):3.7257852720323075):2.917446494181238,((((10:1.5953033375122496,(61:0.9665870770126035,((75:0.45621981466839234,84:0.45621981466839234):0.14964680647902628,81:0.6058666211474185):0.36072045586518475):0.628716260499646):0.2134522222003978,(42:0.4716140718224503,15:0.4716140718224503):1.337141487890197):0.8997073897570069,((59:1.5919713227709713,(62:0.036685891035822024,97:0.036685891035822024):1.5552854317351494):0.9112017219020864,45:2.5031730446730576):0.20528990479659678):4.1827328987753924,16:6.8911958482450455):1.625438220821922):0.04290160183384982):2.2155666934720966,((((40:7.742049283485471,(((30:5.447712491933546,(27:4.768432761392109,(2:0.023258785573133683,98:0.023258785573133683):4.745173975818975):0.6792797305414364):1.0414885888740284,19:6.489201080807572):0.9913835488933127,(14:0.31318111750948685,88:0.31318111750948685):7.167403512191395):0.2614646537845861):2.041711127405002,(((7:3.0552620657889875,1:3.0552620657889875):0.8756660240984575,(32:2.680712210577303,((43:0.2567043296704195,90:0.2567043296704195):0.18084582941697736,85:0.4375501590873969):2.2431620514899056):1.2502158793101419):2.735402194433463,(((18:1.068162533797105,((71:0.1974356248122474,92:0.1974356248122474):0.5887819098285868,79:0.7862175346408341):0.28194499915627097):1.2562768894134346,28:2.3244394232105403):3.492448992506813,23:5.816888415717351):0.8494418686035541):3.117430126569566):0.05466310192621265,(((((6:2.3185653716703074,(52:2.0302096446845277,55:2.0302096446845277):0.2883557269857803):1.083234635779884,(38:0.477288137677902,83:0.477288137677902):2.9245118697722905):0.33592881307072875,((((36:0.11000801045972332,94:0.11000801045972332):1.195507207433223,56:1.3055152178929461):1.2055365149217394,44:2.5110517328146855):0.25778911706077157,5:2.768840849875458):0.968887970645463):2.492773369886628,(22:1.6626455862004434,(60:0.8614108729672463,34:0.8614108729672463):0.8012347132331968):4.567856604207104):2.9531801246484166,((((8:0.9402206812903071,(76:0.7996302558976269,78:0.7996302558976269):0.1405904253926801):2.3719742598172275,39:3.312194941107535):1.7594548846569782,53:5.0716498257645135):1.6748009204392487,((((((17:0.58879229873812,82:0.58879229873812):0.9014753362439138,((65:0.7582492963814058,63:0.7582492963814058):0.3033939026578637,73:1.0616431990392694):0.4286244359427643):0.014853436165981103,64:1.5051210711480152):2.772886055667478,11:4.278007126815494):1.1366596761394698,29:5.414666802954963):1.0880005181144308,(12:0.7161305049699688,80:0.7161305049699688):5.7865368160994235):0.24378342513436804):2.437231568852204):0.6547411977607217):0.2812233750055425,(35:2.465524792770977,47:2.465524792770977):7.654122095051253):0.6554554765506857):4.660990752726407,(3:1.7506050438671765,(58:0.19584257078666348,(93:0.05071457510305551,96:0.05071457510305551):0.14512799568360796):1.5547624730805132):13.685488073232149):0.0; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 5; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 5; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 5; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6732219986260810463 WM1148f47d2081; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7885352486418568017 WM1149667c69b0; checksum 0 905627623 WM1149667c69b0; endTell; getWindow; tell It; setResourcesState false false 72; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1163 648; setLocation 8 22; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 786.1187814845004.4817563795317733133; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1091 581; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; toggleCorners on; 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 on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; toggleGray off; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #7885352486418568017; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; toggleMPRsMode off; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; setCharacter 1; setMapping 1; toggleShowLegend on; toggleGray off; toggleWeights on; setInitialOffsetX -162; setInitialOffsetY -307; setLegendWidth 142; setLegendHeight 158; resume ; endTell; 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; setDigits 4; writeAsPercentage off; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #7885352486418568017 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1091 581; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 16; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; hideWindow; 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.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '../Introduction.nex'; setPrevFileName '07-contTreeSim.nex'; getWindow; tell It; popAsTile false; popOut; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 524 161; setLocation 108 630; setFont SanSerif; setFontSize 10; setExplanation 'This shows a tree and character simulated together. The BiSSE model was used, with rate of speciation with state 0 = 0.1, with state 1 = 0.3, rate of extinction with state 0 = 0.05, with state 1 = 0.05, and rates of state change 0.005.^n^nA block of simulated trees and accompanying matrix (such that the i''th character was simulated with the i''th tree) was made by selecting Trees & Diversification Characters from the Taxa & Trees menu. '; setTitle Simulated_trees_&_characters; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Return_to_main_Intro.; endTell; showWindow; endTell; endTell; end;