#NEXUS [written Fri Sep 22 08:19:34 MDT 2017 by Mesquite version 2.75 (build 564) at geosmac06.local/192.168.136.174] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=36; TAXLABELS Adocus_lineolatus_ Carettochelys_insculpta Cycloderma_aubryi Pelochelys_bibroni Amyda_cartilaginea Cyclanorbis_elegans Rafetus_euphraticus Apalone_ferox Nilssonia_formosus Cycloderma_frenatum Nilssonia_gangetica Nilssonia_hurum Chitra_indica Apalone_mutica Lissemys_punctata Cyclanorbis_senegalensis Pelodiscus_sinensis Apalone_spinifera Palea_steindachneri Dogania_subplanus Trionyx_triunguis Gilmoremys_lancensis Plastomenus_thomasii H._rememdium H._arctochelys H._tetanetron H._sterea Helopanoplia_distincta Aspideretoides_foveatus Atoposemys_superstes Perochelys_lamadongensis Perochelys_hengshanensis_ Gobiapalone_orlovi '''Trionyx'' kyrgyzensis' Nemegtemys_conflata '''Aspideretes'' maortuensis' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; LINK TAXA = Taxa; DIMENSIONS NCHAR=94; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6"; CHARSTATELABELS 1 'Width-length of nuchal bone' / _ less_than_2 greater_than_2 greater_than_3 greater_than_4, 2 Anterior_and_posterior_costiform_processes_of_nuchal_bone_united / _ no yes, 3 Position_of_anterior_edge_of_first_body_vertebra_relative_to_nuchal_bone / _ posterior_edge_of_nuchal middle_of_nuchal anterior_edge_of_nuchal, 4 First_and_second_neurals_fused / _ no yes, 5 Total_number_of_peripherals / _ 22 20 '14-18' 0, 6 Prenuchal_bone / _ absent present, 7 Size_of_eighth_pleurals / _ large reduced_or_absent, 8 Epiplastral_callosity / absent present, 9 Entoplastral_callosity / absent present, 10 'Hyo/Hypoplastral callosity' / absent present, 11 Xiphiplastral_callosity / absent present, 12 Supernumerary_callosities / absent present, 13 Hyoplastra_and_hypoplastra_fuse_just_after_hatching / _ no yes, 14 Extended_midline_contact_of_xiphiplastral_callosities / _ absent present_along_much_of_the_midline, 15 'Hypo-xiphiplastral union' / _ xiphiplastra_lateral_to_hypoplastra hypoplastra_lateral_to_xiphiplastra, 16 Number_of_neurals / _ eight_ seven_ six_or_less, 17 Variability_in_position_of_neural_reversal / _ always_at_same_neural always_at_adjacent_neurals highly_variable, 18 Pleurals_which_meet_at_midline / none eighth_only seventh_and_eighth_or_eighth_only 'sixth, seventh, and eighth or seventh and eighth' 'more than sixth, seventh, and eighth', 19 Point_of_reversal_of_orientation_of_neurals / _ seven_ six five four, 20 Suprascapular_fontanelles / _ closed_at_hatching closed_in_large_adults_only open_throughout_life, 21 Epiplastron_shape / _ 'J-shaped' 'I-shaped', 22 Length_epiplastra_anterior_to_entoplastron_contact / _ short _intermediate long, 23 Depressions_on_eighth_pleurals_for_contact_of_ilia / _ present absent, 24 Bridge_length / _ long short, 25 'Largest adult size 200 mm or less (disc length)' / _ no yes, 26 Carapace_margin_straight_to_concave_posteriolaterally / _ no yes, 27 Sexual_dimorphism_in_disc_length / _ no yes, 28 Jugal_contacts_squamosal / _ no in_one_half_of_sample, 29 Jugal_contacts_parietal_on_skull_surface / _ no in_one_half_of_sample yes, 30 Vomer_contacts_prefrontal / _ yes no, 31 Dorsal_edge_of_aperture_narium_externum_laterally_emarginated / _ no weakly strongly, 32 Dorsal_edge_of_aperture_narium_externum_medially_emarginated / _ no yes, 33 Basisphenoid_contacts_palatines / _ no yes, 34 Vomer_divides_maxillae / _ yes no, 35 Vomer_reaches_intermaxillary_foramen / _ yes no, 36 Vomer_contacts_basisphenoid / _ no occasionally, 37 Size_of_foramen_palatinum_posterius / _ large small small_and_divided many_small_openings, 38 Foramen_palatinum_posterius_forms_in / _ 'palatine and pterygoid and/or maxilla' palatine_only, 39 Foramen_jugulare_posterius_ / _ open enclosed, 40 Separation_of_fjp / _ by_pterygoid by_opisthotic, 41 Foramen_posterius_canalis_carotici_interni_relative_to_lateral_crest_of_basioccipital_tubercle / _ above_ in_it below, 42 Maxilla_contacts_frontal_in_front_of_orbit / _ no yes, 43 Exoccipital_contacts_pterygoid / _ no yes, 44 Basisphenoid_shape / _ not_medially_constricted occasionally_medially_constricted medially_constricted, 45 Premaxilla_absent / _ no occasionally usually, 46 Vomer_lost / _ no yes, 47 Jugal_contacts_orbit / _ yes no, 48 'Epipterygoid, if present, contacts the palatine' / _ yes in_ca._50% no, 49 Contact_between_pterygoid_and_foramen_nervi_trigemini_occurs_when_epipterygoid_is_present / _ yes no, 50 When_epipterygoid_is_present_pterygoid_contacts_foramen_nervi_trigemini / between_epipterygoid_and_quadrate_or_not_at_all between_prootic_and_epipterygoid_or_not_at_all between_epipterygoid_and_parietalor_not_at_all, 51 Epipterygoid_contacts_prootic_anterior_to_foramen_nervi_trigemini / _ no in_ca._50% yes, 52 Epipterygoid_contacts_prootic_posterior_to_foramen_nervi_trigemini / _ no yes, 53 Epipterygoid_fuses_to_pterygoid / _ in_subadults in_adults_only never, 54 Average_ratio_of_intermaxillary_foramen_length_to_length_primary_palate / 0.07 0.20_to_0.40 about_0.60, 55 Postorbital_bar_relative_to_orbit / about_2_times_orbit_diameter 'about equal to orbit to 1/3 of orbit' 'less than 1/5 of orbit', 56 Quadratojugal_participates_in_processus_trochlearis_oticum / _ no yes, 57 Proportion_of_processus_trochlearis_oticum_made_up_by_parietal / _ 15.6%_or_less 22.1%_or_more, 58 Ventral_keel_on_8th_cervical_present_and_limited_to_posterior_end / _ no yes, 59 Strong_dorsal_processes_on_cervicals / _ no yes, 60 Number_of_ossifications_in_corpus_hyoidis / _ 6 8, 61 Number_of_ossifications_in_comu_branchiale_II / _ 1_only '2-6' 7_or_more, 62 Ossifications_of_comu_branchiale_II_broad_and_strongly_sutured / _ no yes, 63 Basihyals_in_close_contact_and_projecting_anteriorly / _ no yes, 64 Symphyseal_ridge_strong_and_present_in_a_depression / _ no yes, 65 Foramen_intermandibularis_caudalis_enclosed_by_prearticular / _ sometimes never, 66 Ilia_curve_medially / _ no yes, 67 Ischia_extend_into_thyroid_fenestra / _ yes no, 68 Metischial_processes_present_and_distinct / _ yes no, 69 Angle_of_acromion_process_to_scapula_approaches_that_of_coracoid_to_acromion / _ no yes, 70 Coracoid_longest_of_three_pectoral_processes / _ no yes, 71 Development_of_surface_sculpturing_of_carapace_and_plastron / all_metaplastic_portions_of_carapace_and_plastron_have_trionychid_sculpturing 'trionychid pattern grades towards the center of carapacial and plastral disk to a smooth pattern, as developed in Hutchemys rememdium and Hutchemys arctochelys', 72 Nuchal_notch / anterior_rim_of_nuchal_convex_or_slightly_notched 'anterior rim of carapace with deep nuchal notch, as developed in H. rememdium', 73 'Shape of neural 1 and 2 (neural 2 and 3 of Meylan 1987)' / neurals_1_and_2_hexagonal_with_short_posterior_sides 'neural 1 circular to rectangular and neural 2 octagonal, as developed in H. rememdium and H. arctochelys', 74 Splitting_of_costals_along_distal_margin / costal_rim_rounded_or_graded 'dorsal rims split into separately protruding dorsal and visceral portions, as developed in H. rememdium and H. arctochelys', 75 Lateral_notch_in_carapace_at_the_level_of_costal_5 / 'absent, lateral carapacial margin rounded' 'present, lateral carapacial margin shows a waist, as developed in H. arctochelys', 76 Skin_callosity_developed_on_the_visceral_side_of_costals_6_and_7 / 'absent, visceral side smooth' 'present, visceral side sometimes develops a callosity, as seen in H. arctochelys', 77 'Mid-line contact of hyoplastra, hypoplastra and xiphiplastra' / 'hyo-, hypo- and xiphiplastra do not contact another fully, even in adults' 'hyo-, hypo and xiphiplastra contact another fully along the entire mid-line in adults, as developed in H. rememdium and H. arctochelys', 78 Shape_of_deep_portion_of_entoplastron / lateral_branches_of_entoplastron_more_or_less_straight_and_merge_anterior_at_a_clear_angle 'entoplastron wide and rounded, as seen in P. aff. thomasii', 79 Mobility_of_entoplastron_and_anterior_development_of_hyoplastron / 'lateral branches of entoplastron abut loosely against hyoplastron, anterior rim of hyoplastron develops no anterior flap/shoulder' 'lateral branches of entoplastron abut loosely against hyoplastron, but hyoplastron develops an anterior flap/shoulder, as seen in Plastomenus aff. thomasii' 'entoplastron tightly integrated into anterior plastral lobe due to strong development of anterior flap/shoulder, as developed in H. rememdium and H. arctochelys', 80 Peripheral_ossification / 'lateral bridge ossification of plastron does not significantly extend beyond the lateral processes of hyo- and hypoplastron' 'lateral bridge ossification of plastron extends laterally beyond bridge processes of the hyo- and hypoplastron and ossifies the peripheral aspects of the shell, as seen in H. arctochelys', 81 Number_of_lateral_hyoplastral_processes / _ one two three_or_more, 82 Extensive_secondary_palate_consisting_of_infolded_maxillae / absent 'present, as developed in Plastomenus thomasii', 83 Accessory_ridges_of_upper_triturating_surfaces / absent present, 84 Posterior_portion_of_narial_canal_defined_by_bone / absent 'present, as developed in Gilmoremys lancensis', 85 Dentary_symphysis_ / short 'extremely long, mandible extremely elongate, as developed in Plastomenus thomasii', 86 Parietal_contribution_to_orbits_ / parietals_neither_contribute_to_orbit_margins_or_orbit_walls 'parietals either contribute to orbit walls, as developed in Gilmoremys lancensis, or orbit margin, as developed in Plastomenus thomasii', 87 Proportions_of_costals_VIII_ / wider_than_long_to_nearly_square significantly_taller_than_wide, 88 Ilium_with_expanded_dorsal_end / present absent, 89 Hyoplastron_with_strongly_serrated_medial_edge / present absent, 90 Serrated_medial_edge_of_hyoplastron_extends_nearly_to_the_posterior_edge_of_bone / present absent, 91 Process_on_medial_edge_of_hypoplastron / of_subequal_size_and_radiating_outward_from_the_medial_edge_of_the_bone with_enlarged_anterior_process_separated_by_a_gap_from_smaller__posterior_processes, 92 Ossification_of_basibranchials / 'poorly ossified, especially posterior pair ' well_ossified, 93 'Metaplastic ossification of hypoplastron "rolls" onto posterior aspects of lateral processes' / absent present, 94 Free_rib_ends / 'all ribs end free, not covered by metaplastic ossification' only_costal_ribs_VII_and_VIII_free all_ribs_covered_by_metaplastic_bone ; MATRIX Adocus_lineolatus_ 2-1-111-----11-312-1-1?-11?1111111-1(1 2)21-1121111?12??3-11121----121112100--001--0-01?00101--0-- Carettochelys_insculpta (1 2)-1-211-----1113?3-1-2?-11?111112111212?112111112?113-11111----122212200---01--0-00000101--0-- Cycloderma_aubryi 212141111110222(1 2)1211211112112221122142213111112(1 2)2-1211111122112122121100000000101000000?01111- Pelochelys_bibroni 322241100110111(1 2)11(2 3)21122111121111112211-2111311210(1 2)121111223221111212200000000002000000?010100 Amyda_cartilaginea 322241101110111111221322111111211221211-211(1 2)111(1 2)10(1 2)1311212132112112112000000000020000001011100 Cyclanorbis_elegans 222141100100212(1 2)121111221111211212213221311111112-1221122112112121222100000000101000000?011?00 Rafetus_euphraticus 322241200100111212(2 3)21122111111212111211-311(1 2)1111101132122213311121221200000000002000000?011100 Apalone_ferox 322241200110111232321122112111311111211-311111111011321221133111112212000000{0 1}0{0 1}010000001011?00 Nilssonia_formosus 222241100110111111211122111221211221211-31121111111131111---2112212---0000000000?000000????100 Cycloderma_frenatum 211141111110212(1 2)122121111211221112214221311122122-12211211221121221211000000001010000001011?10 Nilssonia_gangetica 322141101110111(1 2)22(2 3)11222111111211221211-31121111111121121112311211211200000000002000000?011100 Nilssonia_hurum 322141101110111122(2 3)112221111(1 2)1311221211-3112111111(1 2)131111113111211211200000000002000000????110 Chitra_indica 323241100110111111(2 3)11122112122111111211-21112112102130011223221121212200000000002000000?010100 Apalone_mutica 422241211110111(1 2)323311222122(1 2)1311121211-311111112-1122222112211111212200000000{0 1}01000000?011?00 Lissemys_punctata 211132111110222(2 3)122121111211(1 2)111121122213111111(1 2)11111111111211212112120000000011100000011-1112 Cyclanorbis_senegalensis 3221421111112123-4-111111111222111113221311111122-1211111112112122222100000000102000000?011112 Pelodiscus_sinensis 422241111110111(1 2)323213222112(1 2)13112212222311211111211311211122111112112000000000020000001011100 Apalone_spinifera 322241211110111232331122212111311111211-311(1 2)11112-1132222112311111212200000000{0 1}010000001011100 Palea_steindachneri 222241100110111(1 2)122113222111213112212122311211112-2131211--221111-2---0000000000?000000?????00 Dogania_subplanus 4222411001101111202313222111(1 2)13112212122321(1 2)11111-11212211132112112112000000000020000001011?02 Trionyx_triunguis 322241100110111212(2 3)21122111111311221211-312111111011212221122111112112000000000020000001010100 Gilmoremys_lancensis 42?1411?1110121212-1??2211?22231{1 2}221322(1 2)3111?1112-2131111?????????????0000000?102111110?1-1?00 Plastomenus_thomasii 42?141101110122(2 3)-(2 3)-1?11111?11???12-1222(1 2)3211111??????-211??????1??????10010011102100111???-?10 H._rememdium 42?1411111101222122111?111????????????????????????????????????????21??11110011201?????{0 1}?1--?10 H._arctochelys 42?1411?111012221221??1111????????????????????????????????????????????11111111211?????1?1--?12 H._tetanetron 42?1411?11101122122111?121????????????????????????????????????????????1101001?201?????0???-?12 H._sterea 32?141111110122212(2 3)1111121????????????????????????????????????????????{0 1}0010011211?????1?1--?12 Helopanoplia_distincta 42?1411??110122(1 2)1(1 2)21??2111????????????????????????????????????????????000(0 1)001?111?????(0 1)?1--?11 Aspideretoides_foveatus 42314110011011121221112211????212??12????1?1111??????11?1??2??11??????10000001{0 1}01???0?011-1100 Atoposemys_superstes 42?1411?0110111(2 3)1221??2221????????????????????????????????????????????11010001{0 1}01?????0?1-??01 Perochelys_lamadongensis 4212412000001111?03311?221??2?????????????????1???????1?1?12111??121??00000000002???000?000000 Perochelys_hengshanensis_ ?2??4??00000111?????????21???????????????????????????????????????1?1??0??00000002??????0000?00 Gobiapalone_orlovi 422241200100111(1 2)1232112211?11?211111211231?1?1???????221111????1?1211?000000000020000001011?00 '''Trionyx'' kyrgyzensis' 42??41?000001111???311?221????????????????????????????????????????????00000000002?????0?000?00 Nemegtemys_conflata ?????????1??2???????????????????????????????????????????????????????????????????????????????10 '''Aspideretes'' maortuensis'???24?2000001111?0231??211????????????????????????????????????????????0?00??0000????????000??0 ; END; BEGIN TAXA; TITLE Carettochelys_insculpta; DIMENSIONS NTAX=1; TAXLABELS taxon_1 ; END; BEGIN TREES; Title backbone; LINK Taxa = Taxa; TRANSLATE 1 Adocus_lineolatus_, 2 Carettochelys_insculpta, 3 Cycloderma_aubryi, 4 Pelochelys_bibroni, 5 Amyda_cartilaginea, 6 Cyclanorbis_elegans, 7 Rafetus_euphraticus, 8 Apalone_ferox, 9 Nilssonia_formosus, 10 Cycloderma_frenatum, 11 Nilssonia_gangetica, 12 Nilssonia_hurum, 13 Chitra_indica, 14 Apalone_mutica, 15 Lissemys_punctata, 16 Cyclanorbis_senegalensis, 17 Pelodiscus_sinensis, 18 Apalone_spinifera, 19 Palea_steindachneri, 20 Dogania_subplanus, 21 Trionyx_triunguis, 22 Gilmoremys_lancensis, 23 Plastomenus_thomasii, 24 H._rememdium, 25 H._arctochelys, 26 H._tetanetron, 27 H._sterea, 28 Helopanoplia_distincta, 29 Aspideretoides_foveatus, 30 Atoposemys_superstes, 31 Perochelys_lamadongensis, 32 Perochelys_hengshanensis_, 33 Gobiapalone_orlovi, 34 '''Trionyx'' kyrgyzensis', 35 Nemegtemys_conflata, 36 '''Aspideretes'' maortuensis'; TREE backbone = (1,(2,((36,34,25,24,22,23,35,33,31,30,29,32,27,28,26),((((6,16),(10,3)),15),(((((20,(5,(11,(12,9)))),19),17),(7,(14,(8,18)))),(21,(4,13))))))); END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 94; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 2 4 6 - 15 17 - 19 21 23 - 40 42 - 53 55 - 78 80 82 - 93, ord: 1 3 5 16 20 22 41 54 79 81 94; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1506089974616; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3058359911588649283; tell It; setDefaultOrder 32 44 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 27 34 29 27 29 31 32 34 35; attachments ; endTell; setID 1 7846342624461180338; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 845542372053331179; tell It; setDefaultOrder 0 1 2 3 4 5 6 8 9 10 11 12 13 14 17 15 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 42 40 44 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 63 64 65 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 96 97 98 99 92 93; attachments ; endTell; mqVersion 275; checksumv 0 3 826126290 null getNumChars 94 numChars 94 getNumTaxa 36 numTaxa 36 short true bits 2305843009213693983 states 31 sumSquaresStatesOnly 35132.0 sumSquares -4.6116860184273854E19 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 63; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1120 889; setLocation 410 41; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3058359911588649283 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3058359911588649283; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; columnWidth 0 83; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1057 822; setLocation 410 41; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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.trees.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1057 822; setLocation 410 41; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3058359911588649283 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #3058359911588649283; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 880.1505171319728.662095580539251734; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1057 822; setLocation 410 41; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; toggleWhiteEdges 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; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #845542372053331179 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 110; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1057 822; setLocation 410 41; setFont SanSerif; setFontSize 12; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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 off; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; 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.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; getTable; tell It; rowNamesWidth 707; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1057 822; setLocation 410 41; setFont SanSerif; setFontSize 12; getToolPalette; tell It; setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam; endTell; rowsAreCharacters on; toggleConstrainChar on; toggleConstrainCharNum 3; togglePanel off; toggleSummaryPanel off; endTell; showWindow; 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.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #845542372053331179 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.DefaultCharOrder.DefaultCharOrder; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.lists.CharListPartition.CharListPartition; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; newAssistant #mesquite.parsimony.CharListParsModels.CharListParsModels; getTable; tell It; columnWidth 0 68; columnWidth 1 86; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1057 822; setLocation 410 41; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;