#NEXUS [written Fri Jun 06 02:12:24 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 salmon_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 oflagellida_Salpingoecidae Dictyostelium_fasciculatum Trypanosoma_cruzi Trypanosoma_brucei ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=34; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Homo_sapiens AQAHLKLGEVSVESENYVQAVEEFQSCLNLQEQY Bos_taurus AQAHLKLGEVSVESENYLQAVEEFQACLNLQEQY Mus_musculus AQAHLKLGEVSVESENYIQAVEEFQACLSLQEQY Orcinus_orca AQAHLKLGEVSVESENYIQAVEEFQACLNLQEQY Gallus_gallus AQAHLKLGEVSIESENYVQAIEEFQACLALQQKY Taeniopygia_guttata AQAHLKLGEVSIESENYTQAIEEFQACLALQQKY Xenopus_laevis AQAHQKLGEVCIESENYSQAVEDFLACLNIQKEH Xenopus_tropicalis AQAHLKLGEVSVESENYSQAVEDFLACLNIQKEH salmon_salar AQAHLNLGEVAAESGNYSQAVDDFQQCLSLQLKH Danio_rerio AQIHLKLAEVGVESGNYSQALEDSNECLTLQLKH Maylandia_zebra AQAYLKLGEVSAESGNYPQALDDFQECLALQLKY Oreochromis_niloticus AQAHLKLGEVSAESGNYPQALEDFQECLKLQVKH Takifugu_rubripes AQIYLKLGEVSAESGNYPQALEDFQECLCLQLKH Halocynthia_roretzi AQCHLKLGELGLEVENHPQAIGDFLECLVIQKDL Ciona_intestinalis AQCHSKLGELGLEVENYSQSIGDFLESLVIHKEL Tribolium_castaneum AETLIVLGEISLESGNFTSAIEDMTQGLEIQKTL Danaus_plexippus AEVHLALGEVALESETYDKAVADMISCLDIQKEL Bombus_terrestris SDAYRLLGEVAMEGGNFQGALNDLHRCLELLQQI Megachile_rotundata ADAYRLLGEVAMEGGNFQGALNDLHRCLELLQQI Apis_florea ADAYRLLGEVAMEGGNFQGALNDLHRCLDLLQQI Drosophila_melanogaster AEVQTELANIEFENGILEAAREDYEKALKIHGEL Drosophila_sechellia AEVQTELANIEFENGILEAAREDYEKALKIHGEL Drosophila_erecta AEVQTELANIEFENGILEAAREDYEKALKIHGEL Caenorhabditis_elegans ADVLVLLGEHGISDGKYTQAFEDLDRALNIQRNV Caenorhabditis_remanei ADVLILLGDHGIADENYEQAREDLGRALGIQQNI Caenorhabditis_brenneri ADVLVLLGEHGVSDGKYDQAKEDLEKALEIQKNV Caenorhabditis_briggsae ADVLVVLGDHSVSDGKYDQALEDLEQALEIQKNV Tetrahymena_thermophila VEVTLRIADLEQWRDNFSDALKEYTMALQLSKEI Ichthyophthirius_multifiliis VQVTLRLGDLEAWRDSLKDSVEQYTEALNIAFQI Paramecium_tetraurelia AKVYIKLAELDQWRDKFDDAQENLQKSLQLRLQC Plasmodium_yoelii SYVFIRLGDISLLNHFFEEALKEYEKCVNLREEH Neospora_caninum SFAYVRLADMQLMNERYDEAAQDYREAVSLRERY Toxoplasma_gondii SFAFVRLADMQLMNERYDEAAQDYGEAVSLRERY Albugo_laibachii ARVYMRLGDLSMESENFTRAKQDYENSLVLNKKI Thalassiosira_pseudonana AKVHSRLGDLQKANGNSTGSISDYIISLSIRAKC Schizosaccharomyces_pombe ADIYDLLGELSLEIENFSQASQDLKTALEWKEKV Trichosporon_asahii SECYLALGDVSCETENFDQAVKDYEAAVKLKASL Saccharomyces_cerevisiae GDVYILMGDIEREAEMFSRAIHHYLKALGYYKTL Schizosaccharomyces_japonicus ADVLDLLGEISLENESFEQAAQDLQEALLWKQQV Tetrapisispora_phaffii GDVDQEVEDFATAVEDYKQAIDYIKETDEFENEN Cryptococcus_gattii SDCYLALGNVSCETENFSQAVQDFTAAVDIQNTI Candida_albicans SETYDILGEVSLEAENFNQAADDLRKCLELRLEL Coccidioides_immitis SDIYDLQAEISLEGERFSEAVSDLRAALKLKREL Neurospora_crassa GDLHDLLAEISLENERYPAAITDSRASLKYKQQL Arabidopsis_thaliana VDILCSLAEVSLEREDIESSLSDYKNALSILERL Capsella_rubella VDILCALAEISLEREDIESSLSDYKKALSILERL Theobroma_cacao VDILSALAEVALEREDIESSLSDYQKALSILQQL Cicer_arietinum VDILSTLGDVALEREDFETSLSDYQKALSILEQL oflagellida_Salpingoecidae ADVHFELGSVYLETDQYREAEEELEQCVALRRKW Dictyostelium_fasciculatum SDVHMLLGDLNVELENHQDALEEYNIALQLRKKQ Trypanosoma_cruzi AEVHNSIAQLQVEREDFDSALKEYESELMTYRFI Trypanosoma_brucei AEVHNAIAQVQVEREAYEEALKEYESELFIYRYL ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 34; 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 salmon_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 oflagellida_Salpingoecidae, 50 Dictyostelium_fasciculatum, 51 Trypanosoma_cruzi, 52 Trypanosoma_brucei; TREE Imported_tree_0 = ((((((((((((((((3,4)0.4840,2)0.5690,1)0.7330,(5,6)0.7510)0.8020,(7,8)0.6870)0.3210,(10,(9,(12,(11,13)0.5570)0.6060)0.4120)0.7490)0.6530,(14,15)0.9600)0.5940,17)0.3930,16)0.1840,(25,(24,(26,27)0.4420)0.6170)0.9070)0.0530,(38,40)0.2780)0.0000,((37,41)0.8800,(((18,19)0.5090,20)0.9970,(42,((36,39)0.6470,(43,44)0.6750)0.3000)0.2030)0.1270)0.0100)0.0060,((((32,33)0.9500,31)0.6300,49)0.1710,(((28,29)0.7470,30)0.5270,(50,(34,35)0.2720)0.1090)0.0810)0.0170)0.0760,(48,(47,(45,46)0.8550)0.6130)0.9490)0.1830,(21,(22,23)0.3160)0.9990)0.9830,(51,52)0.9830); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 34; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 34; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1402035144248; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 530868347663718718; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5168037109683670865; mqVersion 275; checksumv 0 3 3415764046 null getNumChars 34 numChars 34 getNumTaxa 52 numTaxa 52 short false bits 1048575 states 1048575 sumSquaresStatesOnly 2.3350997982604E13 sumSquares 2.3350997982604E13 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 700 467; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; endTell; end;