#NEXUS [written Thu Aug 12 19:05:44 ART 2021 by Mesquite version 3.40 (build 877) at Christophe-PC/192.168.56.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=65; TAXLABELS 'Basal_archosauriformes' Pterosauria Grallator Eubrontes Ceratosaurus Carnotaurus Sciurumimus Allosaurus Concavenator Lourinhanosaurus Dilong Santanaraptor Yutyrannus Albertosaurus Daspletosaurus Gorgosaurus Tarbosaurus Tyrannosaurus Juravenator Sinosauropteryx Sinocalliopteryx Pelecanimimus Ornithomimus Shuvuuia Jianchangosaurus Beipiaosaurus Incisivosaurus Protarchaeopteryx Caudipteryx Ningyuansaurus Avimimus Chirostenotes Apatoraptor Microraptor IVPP_V13476 Sinornithosaurus Changyuraptor Zhenyuanlong Velociraptor Dakotaraptor Anchiornis Xiaotingia Eosinopteryx Aurornis Pedopenna Serikornis Caihong Wulong Jinfengopteryx Jianianhualong Epidendrosaurus Epidexipteryx Yi Ambopteryx Archaeopteryx Mamenchisaurus Neosauropoda Tianyulong Kulindadromeus Psittacosaurus Ceratopsidae Scelidosaurus Stegosauridae Ankylosauridae Ornithopoda ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=71; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6"; CHARSTATELABELS 1 'Smooth skin, other than the propatagium' / present absent, 2 'Smooth skin, distribution' / 'non-membraneous, on the body' 'membraneous, forming wings', 3 'Propatagium (i.e., fleshy structure made of skin filling the angle between the humerus and the forearm)' / absent present, 4 'Scaly body skin (i.e., basement scales on the body other than reticulate scales of the hand, distal portion of metatarsals and pes)' / present absent, 5 'Basement scales, morphology' / pebbly polygonal irregular 'arrow-shaped' 'ornamented (with concentric circle within)' shell elliptical, 6 'Basement scales, size' / 'small, ? 10 mm in diameter' 'large, > 10 mm in diameter', 7 'Basement scales, size variation' / 'weak, size of basement scales relatively uniform' 'important, strong variation in size over a small patch of skin', 8 'Basement scales, distribution' / forming_a_pattern 'uniform or random, not forming any pattern', 9 'Basement scales, cluster areas (i.e., clustering of scales of the same size over a small portion of skin. See Bell, 2012)' / absent present, 10 'Basement scales, surface' / smooth striated_or_corrugated 'rugose, pustulose', 11 'Basement scales, width of interstitial tissue (quantified by the ratio between widest interstitial tissue width and adjacent scale maximum diameter)' / 'narrow (i.e., ratio ? 0.3)' 'wide, basement scales widely separated (i.e., ratio > 0.3)', 12 'Basement scales, imbrication in some areas' / absent present, 13 'Basement scales, flowerlike arrangement (tear-shaped scales converging on a minute, central scale)' / absent present, 14 Feature_scales / absent 'present, without underlying osteoderm' 'present, with underlying osteoderm forming an epiosteoderm', 15 'Feature scales, morphology' / subcircular_or_elliptical polygonal irregular 'multi-pointed shield', 16 'Feature scales, number of basement scales surrounding them' / '>15' ?_15, 17 'Feature scales, distribution' / 'regular, forming a pattern (often aligned in irregular rows)' 'sporadic, irregularly distributed ', 18 'Feature scales, surface' / smooth 'corrugated/striated' with_an_apical_nipple, 19 'Feature scales, size variation on the same body part/appendage (limb, tail etc. Quantified by the ratio between smallest and largest feature scale diameters)' / 'weak, feature scales almost all of the same size (ratio > 0.7)' 'important, strong variation of feature scale size (ratio ? 0.7)', 20 'Feature scales, arrangement of adjacent basement scales' / 'uniform arrangement, scales disposed all around the feature scale in an organized way' no_particular_arrangement, 21 'Feature scales, size of adjacent basement scales' / remain_the_same_or_slighty_diminish_in_size_distal_to_the_feature_scales 'strongly diminish in size distal to the feature scale (rosette)', 22 'Feature scales, midline (feature) scales' / absent present, 23 'Polarized/scutate scales' / absent present, 24 'Polarized/scutate scales, distribution' / 'in the ventral portion of the tail (scutate caudoventral scales)' 'in the dorsal portion of the tail (scutate caudodorsal scales)' 'on the pes (scutate pedal scales)' 'on the body other than the tail and pes (scutate body scales)', 25 'Polarized scales, imbrication' / absent present, 26 Epidermal_midrib_or_veins / absent present, 27 'Reticulate scales (on palmar/plantar surface of manus/pes), morphology' / pebbly polygonal, 28 'Reticulate scales, size' / 'small, < 10 mm in diameter' 'large, > 10 mm in diameter', 29 'Podotheca (i.e., metatarsal and pedal phalanges with reticulate, scutate and scutelate scales)' / absent present, 30 Postcranial_osteoderms / absent present, 31 'Postcranial osteoderms, position' / 'restricted to midline of the back and tail, a single row of dermal ossifications' 'present in the midline and/or other portions of the back and tail (no extensive distribution)' 'covering most or all the dorsal portion of the back and tail/forming a shield (extensive distribution)', 32 'Postcranial osteoderms, morphology' / irregular 'subcircular to elliptical, in some cases with central keel (pup-tent like)' 'conical/horn like' 'subtriangular/subquadrangular/polygonal plate-like', 33 'Postcranial osteoderms, surface' / with_irregular_rugosities 'strongly striated, with parallel grooves' 'strongly striated, with grooves converging centrally' granular, 34 'Postcranial osteoderms, morphological diversity along the body (irrespective of size)' / 'weak, roughly the same morphology along the body' 'important, extremely diverse in shape, i.e., presence of scutes, plates and/or spines, etc.', 35 'Plumage (i.e., pycnofibres, monofilaments, branched feathes, and symmetrical to asymmetrical pennaceous feathers)' / 'absent/unfound' present, 36 Plumage_on_the_skull / absent restricted_to_the_dorsal_part_of_the_skull 'on both dorsal and/or ventral parts of the skull' on_the_ventral_parts_of_the_skull_only, 37 Plumage_on_the_neck / absent restricted_to_the_dorsal_part_of_the_neck on_both_dorsal_and_ventral_parts_of_the_neck on_the_ventral_parts_of_the_neck_only, 38 'Plumage on the body (i.e., back and torso)' / absent restricted_to_the_dorsal_part_of_the_back 'on both the dorsal part of the back and ventral part of the torso, covering most of the body', 39 Plumage_on_the_forelimb / absent 'restricted to the proximal portion of the forelimb (part or most of humerus)' 'covering most of or all the forelimb (humerus + ulna)', 40 Plumage_on_the_hindlimb / absent 'restricted to the proximal portion of the hindlimb (part or most of femur)' 'covering most of or all the hindlimb (femur + tibia)', 41 Plumage_on_the_tail / restricted_to_the_proximal_portion_of_the_tail covering_most_of_or_all_the_tail absent_on_the_tail, 42 Filamentous_crest_on_the_tail / absent present, 43 'Plumage, length on the proximal portion of the hindlimb' / short long, 44 'Plumage, main feather type covering the body' / monofilamentous_integuments 'filamentous/plumulaceous feathers' pennaceous_feathers, 45 Monofilamentous_integument / absent present, 46 'Monofilamentous integuments, morphotype' / 'Slender monofilamentous integument (SMFI)' 'Broad non-tubular monofilamentous integument (BMFI)' 'Broad tubular monofilamentous integument (TMFI)', 47 Filamentous_feather / absent present, 48 'Basally joining filamentous feather, morphotype' / 'Basally joining filamentous feather (BJFF)' 'Basally joining shafted filamentous feather (BJSFF)' 'Basally joining branched filamentous feather (BJBFF)' 'Basally joining membranous-based filamentous feather (BJMBFF)' Compound_structures_arising_from_a_basal_plate, 49 Branched_filamentous_feather / 'Radially branched shafted filamentous feather (RBSFF)' 'Bilaterally branched filamentous feather (BBFF)', 50 'Filamentous integuments (monofilaments/filamentous feathers), general length' / short long, 51 Pennaceous_feathers / absent present, 52 'Pennaceous feathers, morphotype' / 'Symmetrical open-vaned feather (SOVF, Morphotype VII)' 'Symmetrical close-vaned feathers (SCVFs, Morphotype IX)' 'Asymmetrical closed-vaned feathers (ASVFs, Morphotype X)', 53 Pennaceous_feathers_on_the_head / absent present, 54 'Pennaceous feathers on the forelimb (remiges), distribution' / absent_on_the_forelimb 'restricted to the distal extremity of the forearm (metacarpals only)' 'on most or all of the forearm (metacarpals + ulna and/or humerus)', 55 'Asymmetical pennaceous feathers on the forelimb (remiges)' / absent present, 56 'Primary remiges on the forelimb, number' / ?_12 '> 12', 57 Secondary_remiges_on_the_forelimb / absent 'present, ? 15' 'present, > 15', 58 Length_of_the_longuest_remige_vs._humerus / '<2' '>2', 59 Alular_pennaceous_feathers_on_the_first_digit / absent present, 60 Pennaceous_feathers_on_the_hindlimb / absent_on_the_hindlimb 'present, not forming a ''hindwing''' 'present, forming a ''hindwing'' (tetrapterygian condition)', 61 Pennaceous_feathers_on_the_tibia / absent present, 62 Pennaceous_feathers_on_the_metatarsal / absent_from_the_metatarsal 'present, ? 12' 'present, > 12', 63 Pennaceous_feathers_on_the_pedal_digits / absent present, 64 Length_of_the_longuest_pennaceous_feathers_on_the_hindlimb_vs._femur / '<1' '>1', 65 'Longuest pennaceous feathers on the hindlimb, position' / 'on the metatarsus and/or the distal part of tibia' 'on the femur and/or the proximal part of tibia', 66 'Asymmetical pennaceous feathers on the hindlimb (remiges), shape' / absent present, 67 'Pennaceous feathers on the tail (rectrices), distribution' / rectrices_absent restricted_to_the_distal_extremity_of_the_tail on_most_of_the_tail_length, 68 'Asymmetical pennaceous feathers on the tail (rectrices), shape' / absent present, 69 Number_of_pairs_of_rectrices_on_the_tail / ?_14 '> 14', 70 Length_of_the_rectrices_vs._tail_length / '<40%' '>40%', 71 Elongated_pennaceous_tail_feather / absent 'present, proximally ribbon-like close-vaned feather (PRCVF)' 'present, rachis-dominant close-vaned feather (RDCVF)' ; MATRIX 'Basal_archosauriformes'1--0??????????????????????(0 1)0?(0 1)2(1 2 3)010------------------------------------ Pterosauria 0111----------------------0000----1(1 2)221(1 2)10(0 1)0111(0 1)-(0 1)0-------------------- Grallator ??????????????????????????00??????????????????????????????????????????? Eubrontes ??????????????????????????00??????????????????????????????????????????? Ceratosaurus ?????????????????????????????10(0 1)(0 1)0????????????????????????????????????? Carnotaurus 1-?0(1 2 6)(0 1)(0 1)(0 1)0(0 2)(0 1)0010010110?0--0???0----0------------------------------------ Sciurumimus 00?1----------------------???0----10020011-0100--10-------------------- Allosaurus ???0(0 1)001000000--------0--0???0----0------------------------------------ Concavenator 00?0??????????????????1(0 2)0?0010----0------------------------------------ Lourinhanosaurus ???00000?00000-------?0--0???0----0------------------------------------ Dilong ???1----------------------???0----1{2 3}????10?10-1{0 1}?-0-------------------- Santanaraptor 00????????????????????????10??????????????????????????????????????????? Yutyrannus 1-?1----------------------???0----1011{1 2}2{0 1}?01111??10-------------------- Albertosaurus ???0(0 1)00(0 1)00100100?1?00?0--0???0----0------------------------------------ Daspletosaurus ???00000001000--------0--0???0----0------------------------------------ Gorgosaurus ???010010?000?????????0--0???0----0------------------------------------ Tarbosaurus 00?00000001000--------0--?00?0----0------------------------------------ Tyrannosaurus ???0(1 2)011000000--------0--1???0----0------------------------------------ Juravenator 1-?0(3 4)000000(0 1)00--------1000???0----10000010-0100--00-------------------- Sinosauropteryx 1-01----------------------???0----1(1 2)112011-{0 1}??1(0 1)?10-------------------- Sinocalliopteryx 1-01----------------------???0----1121221110110--10-------------------- Pelecanimimus 00?1----------------------???0----0------------------------------------ Ornithomimus 00?1----------------------???0----10{1 2}221{1 2}100111??1????????????????????? Shuvuuia ?????????????????????????????0----1?????????10????????????????????????? Jianchangosaurus 1-?1----------------------???0----100100??-0110--10-------------------- Beipiaosaurus 1-?1----------------------???0----1221221??0111??10-------------------- Incisivosaurus 1-?1----------------------???0----1{1 2}222010-10-1?{0 1}11101001?00------10011 Protarchaeopteryx 1-?1----------------------???0----1????110010-1???11?10???????????100?0 Caudipteryx ??11----------------------???0----10222210010-1?{0 1}11(0 1)01012100------10010 Ningyuansaurus 1-?1----------------------???0----1?{1 2}?????????????????????????????????? Avimimus ?????????????????????????????0----1???2???????????1??2????????????????? Chirostenotes ?????????????????????????????0----1?{1 2}???????1????1????????????????????? Apatoraptor ?????????????????????????????0----1???{1 2}???????????1??2??2?????????????? Microraptor 0011----------------------00?0----12222210120-1??11(1 2)121021121201010(0 1)000 IVPP_V13476 1-?1----------------------???0----1????2??1???????1(1 2)???????21{1 2}0?0?????? Sinornithosaurus 1-11----------------------00?0----1222221012100(0 1)0112020?00011000-?1???0 Changyuraptor 1-?1----------------------???0----1{2 3}2222101(1 2)0-1??11{1 2}-2??2??21{1 2}000?20?10 Zhenyuanlong 1-?1----------------------???0----10{1 2}?2?11??{1 2}?{1 2}??01(1 2)-210210???????2???? Velociraptor ?????????????????????????????0----1???2???????????1??2??1?????????????? Dakotaraptor ?????????????????????????????0----1???2???????????1??2??1?????????????? Anchiornis 0001----------------------00?0----12222210120-10?11102001012111???1???0 Xiaotingia 1-?1----------------------???0----122222??1???????1?02???0?21{1 2}10??????? Eosinopteryx 1-?1----------------------???0----12222210110-10?111020?{1 2}002100?-00---- Aurornis 1-?1----------------------???0----1?22???0??0-10?1????????????????????? Pedopenna 1-?1----------------------00?0----1????2??????1??111???????2120??0????? Serikornis 1-11----------------------???0----1222221012??10?111020??0021{1 2}0?1010??0 Caihong 1-?1----------------------???0----1222221012??1(0 2)?11202??{1 2}1121{1 2}111121110 Wulong 1-?1----------------------???0----1{2 3}??2210?{1 2}0-1??11(1 2)021??0021{1 2}????1?0?0 Jinfengopteryx 1-?1----------------------???0----1022{1 2}1100{0 1}?????11?0?????????????20??0 Jianianhualong 1-?1----------------------???0----1?222210??0-1??11(1 2)02??????1??0??21?00 Epidendrosaurus 1-11----------------------00?0----1{1 2}{1 2}{1 2}2{1 2}{0 1}?11??1??11?02??{1 2}?02?21???????? Epidexipteryx 1-01----------------------???0----12222230110-13?11?00-----0------????2 Yi 0101----------------------???0----112{1 2}22??110-1(1 2)?1??00-----0------????? Ambopteryx 0101----------------------???0----111100?0-1??1??0????????????????????? Archaeopteryx 1-11----------------------???0----11222210120-0---1(1 2)121011021{1 2}001020110 Mamenchisaurus 1-?011110?0000--------???0???0----0------------------------------------ Neosauropoda 1-?0(0 1 6)(0 1)(0 1)(0 1)(0 1)(0 2)0111(0 1)(0 1)?0?00(0 1)13001101(0 1)(1 2)(0 2 3)00------------------------------------ Tianyulong 1-?1----------------------???0----10{2 3}10001-0130--10-------------------- Kulindadromeus 1-001010100100--------11100000----1{1 2}{1 2}{1 2}112-00101(0 4)-10-------------------- Psittacosaurus 0000(0 1)000100001011110000--00000----10000001-0120--10-------------------- Ceratopsidae 1-?01101000001(0 1)11(0 2)(0 1)0000--0???0----0------------------------------------ Scelidosaurus 1-?0(0 1)0010000022?1?1??00--0???12(1 2 3)010------------------------------------ Stegosauridae 1-?0100(0 1)000001(0 1)1?(0 1)10000--010?11(2 3)010------------------------------------ Ankylosauridae 1-?01(0 1)1(0 1)1(0 1)0102001(0 1)10100--000?12(1 2 3)010------------------------------------ Ornithopoda 1-00(0 1 2 5)(0 1)(0 1)(0 1)(0 1)(0 1)(0 1)(0 1)(0 1)(0 1)(0 1 2 3)1(0 1)(0 1)1(0 1)0(0 1)0--0(0 1)000----0------------------------------------ ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 71; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 71; END; BEGIN TREES; Title Trees; ID 01759eb8c3213; LINK Taxa = Taxa; TRANSLATE [0] 1 'Basal_archosauriformes', [1] 2 Pterosauria, [2] 3 Grallator, [3] 4 Eubrontes, [4] 5 Ceratosaurus, [5] 6 Carnotaurus, [6] 7 Sciurumimus, [7] 8 Allosaurus, [8] 9 Concavenator, [9] 10 Lourinhanosaurus, [10] 11 Dilong, [11] 12 Santanaraptor, [12] 13 Yutyrannus, [13] 14 Albertosaurus, [14] 15 Daspletosaurus, [15] 16 Gorgosaurus, [16] 17 Tarbosaurus, [17] 18 Tyrannosaurus, [18] 19 Juravenator, [19] 20 Sinosauropteryx, [20] 21 Sinocalliopteryx, [21] 22 Pelecanimimus, [22] 23 Ornithomimus, [23] 24 Shuvuuia, [24] 25 Jianchangosaurus, [25] 26 Beipiaosaurus, [26] 27 Incisivosaurus, [27] 28 Protarchaeopteryx, [28] 29 Caudipteryx, [29] 30 Ningyuansaurus, [30] 31 Avimimus, [31] 32 Chirostenotes, [32] 33 Apatoraptor, [33] 34 Microraptor, [34] 35 IVPP_V13476, [35] 36 Sinornithosaurus, [36] 37 Changyuraptor, [37] 38 Zhenyuanlong, [38] 39 Velociraptor, [39] 40 Dakotaraptor, [40] 41 Anchiornis, [41] 42 Xiaotingia, [42] 43 Eosinopteryx, [43] 44 Aurornis, [44] 45 Pedopenna, [45] 46 Serikornis, [46] 47 Caihong, [47] 48 Wulong, [48] 49 Jinfengopteryx, [49] 50 Jianianhualong, [50] 51 Epidendrosaurus, [51] 52 Epidexipteryx, [52] 53 Yi, [53] 54 Ambopteryx, [54] 55 Archaeopteryx, [55] 56 Mamenchisaurus, [56] 57 Neosauropoda, [57] 58 Tianyulong, [58] 59 Kulindadromeus, [59] 60 Psittacosaurus, [60] 61 Ceratopsidae, [61] 62 Scelidosaurus, [62] 63 Stegosauridae, [63] 64 Ankylosauridae, [64] 65 Ornithopoda; TREE 'Tree0: Strict consensus tree' = (1,(2,((58,((62,(64,63)),(59,((60,61),65)))),(56,57),(3,(4,((5,6),(7,19,(10,(8,9)),(13,(11,(12,((16,14),(15,(17,18)))))),(21,20),((22,23),(24,((25,26),(((51,52,(53,54)),((27,30,28),(29,(31,(33,32))))),(((35,(48,36),34,37,38),(39,40)),(49,50),((47,42),(41,(46,43),(45,44))),55)))))))))))); TREE 'Tree1: Preferred tree with Saurischia (Sauropodomorpha + Theropoda), Juravenator as a basal tetanuran, anchiornithines in Avialae and Deinonychosauria resolved' = (1,(2,((58,((62,(64,63)),(59,((60,61),65)))),((56,57),(3,(4,((5,6),(7,19,((10,(8,9)),((13,(11,(12,((16,14),(15,(17,18)))))),((21,20),((22,23),(24,((25,26),(((51,52,(53,54)),((27,30,28),(29,(31,(33,32))))),((((35,(48,36),34,37,38),(39,40)),(49,50)),(((47,42),(41,(46,43),(45,44))),55))))))))))))))))); TREE 'Tree2: Tree1 with Juravenator as a Compsognathidae (Pei et al., 2020)' = (1,(2,((58,((62,(64,63)),(59,((60,61),65)))),((56,57),(3,(4,((5,6),(7,((10,(8,9)),((13,(11,(12,((16,14),(15,(17,18)))))),((21,20,19),((22,23),(24,((25,26),(((51,52,(53,54)),((27,30,28),(29,(31,(33,32))))),((((35,(48,36),34,37,38),(39,40)),(49,50)),(((47,42),(41,(46,43),(45,44))),55))))))))))))))))); TREE 'Tree3: Tree1 with Ornithoscelida (Baron et al. 2017)' = (1,(2,((56,57),((58,((62,(64,63)),(59,((60,61),65)))),(3,(4,((5,6),(7,19,((10,(8,9)),((13,(11,(12,((16,14),(15,(17,18)))))),((21,20),((22,23),(24,((25,26),(((51,52,(53,54)),((27,30,28),(29,(31,(33,32))))),((((35,(48,36),34,37,38),(39,40)),(49,50)),(((47,42),(41,(46,43),(45,44))),55))))))))))))))))); TREE 'Tree4: Tree1 with anchornithines as Troodontidae (Hu et al. 2009)' = (1,(2,((58,((62,(64,63)),(59,((60,61),65)))),((56,57),(3,(4,((5,6),(7,19,((10,(8,9)),((13,(11,(12,((16,14),(15,(17,18)))))),((21,20),((22,23),(24,((25,26),(((51,(53,54),52),((27,28,30),(29,(31,(33,32))))),((((48,36),34,35,37,38),(39,40)),((((47,42),(41,(46,43),(45,44))),(49,50)),55))))))))))))))))); TREE 'Tree5: Tree1 with troodontids as sister to (Dromaeosauridae + Averaptor) (Motta et al. 2020)' = (1,(2,((58,((62,(64,63)),(59,((60,61),65)))),((57,56),(3,(4,((5,6),(7,19,((10,(8,9)),((13,(11,(12,((16,14),(15,(17,18)))))),((21,20),((22,23),(24,((25,26),(((51,52,(53,54)),((27,30,28),(29,(31,(33,32))))),((49,50),((39,40),((35,(48,36),34,37,38),(((42,47),(41,(46,43),(45,44))),55))))))))))))))))))); TREE 'Tree6: Tree1 with Troodontidae as sister clade of Avialae (Foth & Rauhut, 2017)' = (1,(2,((58,((62,(64,63)),(59,((60,61),65)))),((56,57),(3,(4,((5,6),(7,19,((10,(8,9)),((13,(11,(12,((16,14),(15,(17,18)))))),((21,20),((22,23),(24,((25,26),(((51,(53,54),52),((27,28,30),(29,(31,(33,32))))),((((48,36),34,35,37,38),(39,40)),((49,50),(((47,42),(41,(46,43),(45,44))),55)))))))))))))))))); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1628805944565; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2596558468995142235; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5005326027684317780; mqVersion 340; checksumv 0 3 3664722417 null getNumChars 71 numChars 71 getNumTaxa 65 numTaxa 65 short true bits 2305843009213694079 states 127 sumSquaresStatesOnly 20663.0 sumSquares -3.1820633527148977E20 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 152; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1366 649; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #2596558468995142235 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #2596558468995142235; getWindow; tell It; useTargetValue off; setTargetValue ; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1214 577; setLocation -8 0; 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; useTargetValue off; setTargetValue ; 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; getTable; tell It; rowNamesWidth 836; columnWidth 1 49; columnWidth 2 65; columnWidth 3 116; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1214 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; setActive; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #2596558468995142235 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 01759eb8c3213; toggleUseWeights off; endTell; setAssignedID 1047.1590678993231.7682690765686811644; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1214 577; setLocation -8 0; 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.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 6; 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 posteriorProbability; toggleShow bootstrapFrequency; 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; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #5005326027684317780 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1214 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; 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 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; toggleShowPaleExcluded 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.AlterData.AlterData; tell It; toggleBySubmenus off; endTell; getEmployee #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1214 577; setLocation -8 0; setFont SanSerif; setFontSize 10; 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; endTell; end;