#NEXUS [written Fri Jun 06 02:26:50 EDT 2014 by Mesquite version 2.75 (build 564) at VampireS-PC/192.168.0.14] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=52; TAXLABELS Homo_sapiens Bos_taurus Mus_musculus Orcinus_orca Gallus_gallus Taeniopygia_guttata Xenopus_laevis Xenopus_tropicalis Salmo_salar Danio_rerio Maylandia_zebra Oreochromis_niloticus Takifugu_rubripes Halocynthia_roretzi Ciona_intestinalis Tribolium_castaneum Danaus_plexippus Bombus_terrestris Megachile_rotundata Apis_florea Drosophila_melanogaster Drosophila_sechellia Drosophila_erecta Caenorhabditis_elegans Caenorhabditis_remanei Caenorhabditis_brenneri Caenorhabditis_briggsae Tetrahymena_thermophila Ichthyophthirius_multifiliis Paramecium_tetraurelia Plasmodium_yoelii Neospora_caninum Toxoplasma_gondii Albugo_laibachii Thalassiosira_pseudonana Schizosaccharomyces_pombe Trichosporon_asahii Saccharomyces_cerevisiae Schizosaccharomyces_japonicus Tetrapisispora_phaffii Cryptococcus_gattii Candida_albicans Coccidioides_immitis Neurospora_crassa Arabidopsis_thaliana Capsella_rubella Theobroma_cacao Cicer_arietinum choanoflagellida_Salpingoecidae Dictyostelium_fasciculatum Trypanosoma_cruzi Trypanosoma_brucei ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=119; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Homo_sapiens GEAFFFYGKSLL-ELARMENGVLGNALEGVHV-EEEE----GEKTEDESLVENNDNIDETEGSEEDDKENDKTEEMPNDSVLENKSLQENEEEE---IGNLELAWDMLDLAKIIFKRQ- Bos_taurus GEAFFFYGKSLL-ELARMENGVLGNALEGVHV-EEEE----GEKTEEESLVENNDNIDETEGSEEEDKENDKAEETLNDSALENKSLQENEEEE---IGNLELAWDMLDLAKIIFKRQ- Mus_musculus GEAFFFYGKSLL-ELARMENGVLGNALEGVHV-EEEE----GEKTEDESLVENNDNVDETEGSEEEDRENDKAEETPNESVLEKKSLQENEEEE---IGNLELAWDMLDLAKIIFKRQ- Orcinus_orca GEAFFFYGKSLL-ELARMENGVLGNALEGVHV-EEEE----GEKTEEETLVENNDNIDETEGSEEEDKENDKAEETPNDSLLENKSLQENEEEE---IGNLELAWDMLDLAKIIFKRQ- Gallus_gallus AEAFFYYGKSLL-ELARMENGVLGNALEGVQVEEE------GEKAEDDSALPAVDET-----EESEEEDKENDKAEDDKENELAVEDKESEEEE---IGNLELPWDMLELAKVIYKRQ- Taeniopygia_guttata AEAFFYYGKSLL-ELARMENGVLGNALEGVQ--VEEE----GEKAEDDSALPAADET-----EESEEEDKENDKADDDKENELTVEDKESEEDE---IGNLELAWDMLELAKVIYKRQ- Xenopus_laevis AEAFYSYGMSLL-ELARLENGVLGNALEGMPE-DDEE----EAEKEEDPNIPSADNLDEKERPEKMEEEEEGEDSEENEDENEGTEEKETEEED---VGNLQLAWEMLDLCKIIFKRQ- Xenopus_tropicalis ADAFYSYGMSLL-ELARMENGVLGNALEGM---PEDE----EDGEKEDPNIPSADNLDEKEREGEEEEGEDSEENDEGTEENEGTEEKETEEED---VGNLQLAWEMLDLCKLIFKRQ- Salmo_salar GEAFFLCGKALL-ELARMENGVLGNALTGVPE-EEEG----EEEKPKDSNIESTDNVDEKTRTKESSDNPEEEDGDVEDGEEKEDIPEDSDDEE---VGNLQLAWEMLEVAKVIYKRK- Danio_rerio GEAFFFCGKALL-ELARMENTVLGNALEGVPE-ESSE----EGEKQDDSKIESADNLDEKTRGDDDGDEDEDDDDDDDEDAEGDAKDKESEEDE---VGNLQLAWEMLEVAKVIYKRK- Maylandia_zebra GEAFFLCGKSLL-ELARMENSVLGNALEGVP--EESE----EEEQPSSSNVESPDNLDDD--DDDDDDDDDDDDDDGEKNGQDKASSYRTEEEE---VGNLQLAWEMLEVAKVIYKRK- Oreochromis_niloticus GEAFFWYGKALL-DLARMENSVLGNALEGV---PEEE----EEEKPKDSNVESTENVDEKTREEEGGDDVEMEGDAEEQGEGDSTGEKDSDDEE---VGHLQLAWEMLEVAKVIYKRK- Takifugu_rubripes GEALFLCGKSLL-ELARMENSVLGNALEGVP--EESE----GEEQPTDSKIESADNLDEKTRAEEEDEGAEGNDDDSDEDDEAGEGNGQAKEEE---VGNLQLAWEMLEVAKVIYKRK- Halocynthia_roretzi CEAYYYYGVSLL-ELARLENGVLGNALKGVPEEDADG----DSDQEQEQFEKPDLPETEREKSSDKPVESSNTEEPGTSGTSASSSKENESEEDPDDISNMQLAWEMLELAKVLYKKH- Ciona_intestinalis AESFYFYGKALL-ELARVENGVLGNALKGVPQVEEAS----SESEGEGNQFEKTKNLPVEKRPADTSDVPMEADEPSTSGGVKDEDVKDEDTEDPDDVPNMQLAWEMLELAKVLYQKK- Tribolium_castaneum GDVYLYYGKSLL-ELSRKESGPLGDGVLKNVEEESET----EDVEENEAGEEESKPVNGETPEEEDDKPPAEGETDQKVEESGSSEEKKEGEETEDELTDLQVAWEVLELAKRIFTNR- Danaus_plexippus AEAYLWYGKSLL-GLSREENGYLGDGVAGGNNEDGDN----EEENGEENAEAEQKNGEIATEEPGSSTENEEKPGTSNGDVNDDSVVNLDNEDD---VDNLQLAWEMLDLSRNILQKR- Bombus_terrestris GEPYLLYGRALL-GLAREEAGVLGGGVPGTEE-TEED----DEEDEEEAEDEKLSNVDEKEENGPSCSTEQNGVVEENGENDGEDIEKEDEEDE---VNNLQVAWEVLELAKLVLLKR- Megachile_rotundata GEPYLLYGRALL-GLAREEAGVLGGGVPGNED-SVED----DEEDEEEVEDEKLSNVDEKEENGPSCSTTEQNGDAKENGDDGEDIGKEDEDDE---VNNLQVAWEVLELAKLVLLKR- Apis_florea GEPYLLYGRALL-GLAREEAGVLGGGVPGTEE-TEED----DEEDEEEAEDEKLSNIDEKEDNGPSCSSDHNGDVKKNGENDGEDIGNEDEEDE---VNNLQVAWEVLELAKLVLLKR- Drosophila_melanogaster GQPLLLYAKALI-AMALDENKVIDVPDEAADD-DDED----VDDDEEESAEDGAAKKEEKKDNDDERPSTSNGEVTASCSNGAAPAVEEEPEEEEGVSGSLQLAWEILEAAAQIFSRQ- Drosophila_sechellia GQPLLLYAKALI-AMALDENKVIDVPDEAADD-DDED----VDDDEEESVEDGAAKKEEKKDNDDERPSTSNGEVTASCSNGAAAAGEEEPEEEEGVSGSLQLAWEILEAAAQIFSRQ- Drosophila_erecta GQPLLLYAKALI-AMALDENKVIDVPDEAADD-DDED----VDDDEEESAEDGPAKKEEKKKNDDERPSTSNGEVTASCSNGAAAAGEEEPEEEEGVSGSLQLAWEILEAAAQIFSRQ- Caenorhabditis_elegans FDSLYYYGMATL-ELAKEESQLLKGP---------------GEKESGDEEQAG---------NSDDKTDEENGETEKEDGEE----SGEEEDDD---DDTMKLSWEILETARCIAAAK- Caenorhabditis_remanei FDACYYYGMASL-EVAKLESALLKNPD--------------EKQRNGVSGDEEAASGDEEEKAEDENDDGSEKED-----------GEESEDDD---EDSMKLAWELLETARCTAAAK- Caenorhabditis_brenneri FDAYYFYGMATL-ELAKVETQLLKN----------------DKDKELDREEEEDTCADEKA-TESKENGDESDEEE----------GEESSEED---DDNMRLAWELLETCRCIAIVK- Caenorhabditis_briggsae YEYYYYYGMATL-ELGKIQGQVFNAPN--------------EKEDNGEAQNSAAGTITNEKGGDGENSEKEDGEES-------------GDEED---DDTMKLAWEVLENARCIAMAK- Tetrahymena_thermophila SKYFFFYGDMLL-SKLENNPDVFGDKAQKKLD-NQTT----EEVEKNPNQMASEEASEQKMVRDETNAPQNNEENQTEENNLPIGKVTMEKSDP---IDDLQLAWENLELSRKIYNQE- Ichthyophthirius_multifiliis SKYYYYYGDMLLTKQDQEEDEN-----------QNEN----KNENENQNENENQINQDEKIITILYKDNGVQIQEEKINGNQEEQKEQNLVQQK---IDDLQLAWENLELCKKIIYKN- Paramecium_tetraurelia AEYYYMYGTIIV-LKLSEQQDVFG-----------------QRTREAENNALGVQDPEDTQ-SENEGEQIEDGDIEEEHKVQENKPHENIED-----LDDFHIAWENLEVARVILEKE- Plasmodium_yoelii REYYLCFADALL-TKEEEKNDLF-------------------------------EFLKKKKSEVTEDEDGSNKEE----------------------VTDEQLAFEMFEFSRKCYEML- Neospora_caninum STYYLWFGDALL-TKEEQNAELFQF--------DKTK----QEAAESGAPSSGAESSASSSSASGSSSSTEKGAHSEEEVPGGNAAGK---------VSDEELAFEMLEMAKRCLLKK- Toxoplasma_gondii STFYLWFGDALL-TKEEQNAELFQF--------DKAK----QDAESGAAAASSAAPASSSS-ATSSSSSTDKGTERHEEEVPGGNAAGKVSDEE--------LAFEMLEMAKQCLLKK- Albugo_laibachii APIYYEYGNALL-SLVEGTANVFGNVLDGS--------------------------------EKHSDKGTDHGQEEKSSQFRNESDDNPIEENVV--KDDLELAWEMLEVARVIYTRH- Thalassiosira_pseudonana APLYYLYGTTLL-YLVEESDVMMNG--------KGEI----QVNDNEDDNDE----------SPPAAHSPQDEEEE----------EEEAPSDP---AEDLQIAWENLETARSIMSKM- Schizosaccharomyces_pombe RNVLWLYGKSLF-QIAIENSQVLGNALGAKESVSQAT----ESFEEPEAIGSFTFSGQKIENYTVNEENSSIAHPEKESEEKETNEASPASEED---EDDFNVAWEVLDLTRVMQSKA- Trichosporon_asahii APLLLSYGKALY-ELALSQQGVMGREE------VAKS----TNPAAAEPSAPAAKGNFVFEGGDDGDEEEEGEGEEQEGEGDGKGQQEEGEEEP---EDDFNAAWEVLDVARTIYTRE- Saccharomyces_cerevisiae PELFTIFAQAVYNMEVQNSGNLFGDALLAGDDGSGSE----SESEPESDVSNGEEGNENGQTHELANFSPANEHDDEIEDVSQLRKSGFHIYFE---NDLYENALDLLAQALMLLGRP- Schizosaccharomyces_japonicus RNVLWLYGRTLF-EIALSKSQVLGGGITPAIE-EQQQ----KETDSGPTVVGSFAFTGDKLETATSEAASSNGSEKTEAATAASPTPAAAVAAE----DDFGLAWEVLDLCRVLQTRA- Tetrapisispora_phaffii PDHVMLLASCLY-QLGVEKNDMFGGGMDDSEGEDDDG----QNEDWVSDDGQDDEDADNKDTSELEQDNSDNENHDPEDDIDEEGLISYVDYLE---GDHFQNTLELLQVARIIYMEN- Cryptococcus_gattii APLLLAYGKALY-DLASSQASVMGREEPVRQE-DDVP----AETNNPNFVFSGDAPSDDEGEDEPEPEVEPQASSSSAPAPAPDAAEGDEMEEL---EDDYNAAWEVLDVARTIYQKI- Candida_albicans ADLLFLYGKAVF-QSGVSKSEVFGGKP------AEPE----VETENSESKEEESKPETDKTDTFQFYADGDGEEEDGEENEEPNEDENNDEDAN---KSDFEVAWELLDLARALFEEK- Coccidioides_immitis ADLLYSYGRCLY-HVAVSKSDVFGSKAAIQNVVESSKPRGKESSNQPQFFMPQSDKNDTSMEKTYFQFNGDENFDDDDEDEEDAGDTGREALVE---DDDFENAFETLDMARVLLSRQ- Neurospora_crassa AEILFLYGRALF-KVGQSKSDVLGGRA------PEPK----PEKKAAKSKKQKKAATEEKEAEGDENFDDSDKEEEDDDEDAE---EGEEEDED---DDDLAVAFQVLDLARVLFEKKL Arabidopsis_thaliana INAYYRYGLALL-AKAQAEADPLGNMPKKEGEVQQES----SNGESLAPSVVSGDPERQGSSGQEGSGGKDQGEDGEDCQDDDLSDADGDADED---ESDLDMAWKMLDIARVITDKQ- Capsella_rubella VNAYYRYGSALL-EKAQAEADPLGNVPKKEGEVQQES----SSKDDSVKNTVNGESLAASVVGQEGAGGIEQGEDGENCHDDDLSDADGDEDDS-----DLDMAWKMLDIARAITDKQ- Theobroma_cacao LKAYYLYGRALL-YKAQEETDPLVSVPKKEGETQQGS----NKEESVKSAVNGESSVASVSSTQHEGATKDGGRDEEEEDEDSDTDDVAEADED---DSDLDLAWKMLDVARAIADKQ- Cicer_arietinum VHTYYKYGCALL-YKAQEEADPLGVVPKKQDVPQHGS----EKDGSVKSAMNAESSTASFPNRESEVVNATSGKNDQEDGGDSDAEDLAEGDED---ESDLDLAWKMLDIARAIVEKQ- choanoflagellida_Salpingoecidae ARVYQLYGLCLI-ASARKEAPMMAAEDLMRLADPSAQ----AAAPSAAPAASAASASSTSKGLDDDDEGDGDEKAGDNQQEGQAAEGDGEQEDD---ASLVQVGWECLECARVIYSRL- Dictyostelium_fasciculatum APIYIKYGRALLFSYKVNESDVLGSKL------DNNK----EGAQEGEPDEAGEDELDKKEASSSDGEDTSTSTSNATTSTTTTTGEKKEEGDK---AETLEVAWDVLELARVIYEKN- Trypanosoma_cruzi GVYFLDYGLSQL-RVLQSKSTV----------------------------------------------------------------EAALQPLD---QDALEACFINLDVARVCFQKQ- Trypanosoma_brucei GIYFLDYGLSQL-RMIQSASSM----------------------------------------------------------------EAALDPLD---HDALEACFTNLDVARVCFQKQ- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 119; END; BEGIN TREES; Title Imported_trees; LINK Taxa = Taxa; TRANSLATE 1 Homo_sapiens, 2 Bos_taurus, 3 Mus_musculus, 4 Orcinus_orca, 5 Gallus_gallus, 6 Taeniopygia_guttata, 7 Xenopus_laevis, 8 Xenopus_tropicalis, 9 Salmo_salar, 10 Danio_rerio, 11 Maylandia_zebra, 12 Oreochromis_niloticus, 13 Takifugu_rubripes, 14 Halocynthia_roretzi, 15 Ciona_intestinalis, 16 Tribolium_castaneum, 17 Danaus_plexippus, 18 Bombus_terrestris, 19 Megachile_rotundata, 20 Apis_florea, 21 Drosophila_melanogaster, 22 Drosophila_sechellia, 23 Drosophila_erecta, 24 Caenorhabditis_elegans, 25 Caenorhabditis_remanei, 26 Caenorhabditis_brenneri, 27 Caenorhabditis_briggsae, 28 Tetrahymena_thermophila, 29 Ichthyophthirius_multifiliis, 30 Paramecium_tetraurelia, 31 Plasmodium_yoelii, 32 Neospora_caninum, 33 Toxoplasma_gondii, 34 Albugo_laibachii, 35 Thalassiosira_pseudonana, 36 Schizosaccharomyces_pombe, 37 Trichosporon_asahii, 38 Saccharomyces_cerevisiae, 39 Schizosaccharomyces_japonicus, 40 Tetrapisispora_phaffii, 41 Cryptococcus_gattii, 42 Candida_albicans, 43 Coccidioides_immitis, 44 Neurospora_crassa, 45 Arabidopsis_thaliana, 46 Capsella_rubella, 47 Theobroma_cacao, 48 Cicer_arietinum, 49 choanoflagellida_Salpingoecidae, 50 Dictyostelium_fasciculatum, 51 Trypanosoma_cruzi, 52 Trypanosoma_brucei; TREE Imported_tree_0 = (((((((((((((2,4)0.6520,3)0.5070,1)0.9960,(7,8)0.9870)0.4270,(5,6)0.9910)0.4780,((9,12)0.4450,(13,(10,11)0.5480)0.3450)0.8470)0.7140,(14,15)0.7690)0.5720,(16,(17,(19,(18,20)0.5350)0.9500)0.3350)0.2240)0.2790,(49,(21,(22,23)0.5480)0.9990)0.4390)0.1960,(27,(26,(24,25)0.4110)0.4570)0.9850)0.1780,(((30,35)0.2780,(34,50)0.2360)0.0300,(((45,46)0.8960,(47,48)0.6470)0.9950,((28,29)0.5300,(31,(32,33)0.9740)0.7710)0.2690)0.0620)0.0230)0.0020,(((36,39)0.9840,(37,41)0.9500)0.1460,((42,44)0.3540,(43,(38,40)0.7130)0.2780)0.0470)0.1510)1.0000,(51,52)1.0000); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 119; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 119; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1402036011031; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8067077859390899891; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3032099695040768155; mqVersion 275; checksumv 0 3 506292535 null getNumChars 119 numChars 119 getNumTaxa 52 numTaxa 52 short false bits 1048575 states 1048575 sumSquaresStatesOnly 4.64935518915E13 sumSquares 4.64935518915E13 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 500; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; endTell; end;