#NEXUS [written Sat Apr 25 20:48:54 EDT 2015 by Mesquite version 2.75 (build 566) at Macintosh-99.local/10.0.1.3] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=76; TAXLABELS Adiantum_aleuticum_WCLG Adiantum_raddianum_BMJR Alsophila_spinulosa_GANB Amborella_trichopoda_scaffold00079.32 Anemia_tomentosa_CQPW Angiopteris_evecta_NHCM Aquilegia_coerula_Aquca_00292.1 Arabidopsis_thaliana_AT1G49140 Argyrochosma_nivea_XDDT Asplenium_nidus_PSKY Asplenium_platyneuron_KJZG Athyrium_filixfemina_URCP Athyrium_sp_AFPO Azolla_caroliniana_cf_CVEG Blechnum_spicant_VITX Bolbitis_repanda_JBLI Botrypus_virginianus_BEGM Crepidomanes_venosum_TWFZ Cryptomeria_japonica_DSXO Culcita_macrocarpa_PNZO Cystopteris_fragilis_LHLE Cystopteris_protrusa_YOWV Cystopteris_reevesiana_RICC Cystopteris_sp_XXHP Cystopteris_utahensis_HNDZ Davallia_fejeensis_OQWW Dennstaedtia_davallioides_MTGC Deparia_lobatocrenata_FCHS Didymochlaena_truncatula_RFRB Diplazium_wichurae_UFJN Dipteris_conjugata_MEKP Encephalartos_barteri_GNQG Equisetum_diffusum_CAPN Equisetum_hyemale_JVSZ Gaga_arizonica_DCDT Gymnocarpium_dryopteris_HEGQ Homalosorus_pycnocarpos_OCZL Hymenophyllum_bivalve_QIAD Hymenophyllum_cupressiforme_TRPJ Leucostegia_immersa_WGTU Lindsaea_linearis_NOKI Lindsaea_microphylla_YIXP Lygodium_japonicum_PBUU Myriopteris_rufa_GSXD Nephrolepis_exaltata_NWWI Notholaena_montieliae_YCKE Onoclea_sensibilis_HTFH Ophioglossum_sp_QHVS Osmunda_sp_UOMY Parahemionitis_cordata_ZXJO Peperomia_fraseri_XSZI Phlebodium_pseudoaureum_ZQYU Phymatosorus_grossus_ORJE Pilularia_globulifera_KIIX Pityrogramma_trifoliata_UJTT Plagiogyria_japonica_UWOD Pleopeltis_polypodioides_UJWU Polypodium_amorphum_YLJA Polypodium_glycyrrhiza_CJNT Polypodium_hesperium_B_IXLH Polypodium_hesperium_GYFU Polystichum_acrostichoides_FQGQ Psilotum_nudum_QVMR Pteridium_aquilinum_Pt_Contig4243 Pteris_ensiformis_FLTD Pteris_vittata_POPJ Sceptridium_dissectum_EEAQ Sticherus_lobatus_XDVM Thelypteris_acuminata_MROH Thyrsopteris_elegans_EWXK Tmesipteris_parva_ALVQ Vittaria_appalachiana_NDUV Vittaria_lineata_SKYV Woodsia_ilvensis_YQEC Woodsia_scopulina_YJJY Zea_mays_GRMZM2G173277_T02 ; END; BEGIN CHARACTERS; TITLE NDUFS6; DIMENSIONS NCHAR=396; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Adiantum_aleuticum_WCLG ATGGGATTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCAGAGGACTTCGATCCTGCGGACCCCTACAAGGACCCGGTGGCATTCCTGGAGATGCGAGAGCACATTGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGTGTGCGCCAATGCTACCGCCGCGAGGGCGTTAACCACCTTCAGAACTGCCGTACAGTTGTTCGTCACTACTTGGAATCACTCAAGGGCATTGGCTGGGGTAAGGAGG-------------------------------------------------------------------------------------------------------------------------------- Adiantum_raddianum_BMJR ----------------------------------------------------------------------------------TGGCATTCCTGGAGATGCGAGAGCACATTGTGCGCGAGAAGTGGGTGGCCATTGAGCGCGCCAAGATTTTGCGTGAACGTGTGCGCCAATGCTATCGTCGTGAGGGCGTTAACCACCTTCAGAACTGCCGTACCACTGTTCTTCAATACTTGGAATCTCTCAAGGGCGTTGGCTGGGGAAAGGAGGGCCGCCCTGCCTATGCCCACGA---------------------------------------------------------------------------------------------------------- Alsophila_spinulosa_GANB ATGGGGTTTAAG---GGC---GTGAAGTTCGACGAGGCGCCCCCGGACGATTTCGATCCGGCGGATCCCTACAAGGACCCGGTGGCGTTTCTGGAGATGCGGGAGCATGTGGTTCGGGAGAAGTGGGTGGCCATCGAGCGCGCCAAGATCTTGCGGGAGCGCGTTCAGCAGTGCTACCGCCGGGAGGGCGTGAACCACCTCCAGAACTGCCGTACCGCCGTCCGCCAGTACTTGGAATCTCTCAAGGGCGTCGGCTGGGGGAAGGAGGGCCGC?--------------------------------CCCGCCACTCCACCCCCGCCACTGCCCTCCGCAAGGGCTTCTTAA--------------------------------------------- Amborella_trichopoda_scaffold00079.32 ATGGTTCGGAAGGCGACT---GTTGAGTTCGATGAGGGACCTCCTGATGACTTCGACCCCAACAACCCCTATGCCGACCCTGTGGCCATGTTAGAGTACAGGGAGCACCTTGTGAGAGAGAAATGGATCCAAATTGAGACGGCTAAGATCTTGAGAGAGAAACTCAAGTGGTGCTATCGCGTAGAGGGGGTGAACCACCTTCAGAAGTGCAGGCACCTCGTCCAACAATACCTCGATGCCACACGTGGGGTTGGCTGGAACAAAGAGAATAGACCTCCTGGTCTTCAT---------------------------------------------GTTTTTCTAGCTGGAATTAGGTATGGGATGGTTGGTTGTTGA--------------------- Anemia_tomentosa_CQPW ATGGTTTTCAAG---GGC---GTGAAGTTTGACGAGGGCCCCCCCGAGGACTTCGACCCGCAGGATCCTCGCAAGGACCCCGTGGCCTACCTGGAGATGCGCGAGTACTTGGTTCGCGAGAAGTGGGTGCAGATCGAGAAGGCCAAGATACTGCGCGAGCGTGTCCGCAATTGCTACCGCCGTGAGGGCGTCAACCACCTTCAGAAATGCCGCAAGGCAGTGCGCCAGTACCTCGCCTCGCTCAAGGACGTGGGATGGGGCAAAGATGGACGCCCTGCCTGGGCCAAC---------------------------------------------AACATCGAGGAGTGA------------------------------------------------ Angiopteris_evecta_NHCM ---------------------------------------CCCCCTGATGACTTCGATCCCCAGCATCCCTACAAGGATCCCATTGCGATGCTCGAGCAGCGGGAGCACGTCGTCCGAGAAAAGCTGATCGCCATCGAGACGGCGAAAATCCTCCGAGAAAGGGTGAAGCAATGCTACAGGCGGGAAGGCGTGAACCATCTCCAAAACTGCAGGCAGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Aquilegia_coerula_Aquca_00292.1 ATGGGAAGGAAGAAGACA---GTGGAATTCGATGAAGGACCACCAGATGATTTCGATCCAAACAATCCATACAAAGATCCAGTAGCAATGTTAGAAATGAGAGAACATTTAGTTCGAGAGAAATGGATTCAAATCGAAACAGCTAAGATTTTAGGGGAAAAGTTGAAATGGTGTTATCGAATTGAAGGTGTTAATCATCTACAGAAATGCAAACATCTTGTTCAACAATATCTTGATTCAACTCGTGGTGTTGGTTGGGGTAAAGATCATCGTCCTACTTGGATGCATGGTCCTAAG------------------------------------GAGGCTGCGGCAGAAGTCGCTGAGTGA------------------------------------ Arabidopsis_thaliana_AT1G49140 ATGGGGAGGAAGAAGGGATTGCCGGAGTTCGAAGAGTCGGCGCCGGATGGATTCGATCCTGAGAATCCGTACAAGGATCCGGTTGCGATGGTGGAGATGAGAGAACACATTGTTCGTGAGAAATGGATCCATATCGAGAAGGCTAAGATCTTACGTGAGAAGGTCAAATGGTGTTACCGCGTCGAAGGCGTTAACCATTACCAGAAGTGTCGTCATCTTGTTCAGCAGTATCTCGATGCCACTCGCGGCGTTGGTTGGGGCAAAGACCACCGTCCTATCTCTCTTCACGGTCCTAAG------------------------------------CCAGTAGCTGTTGAAGAAGCTGAATGA------------------------------------ Argyrochosma_nivea_XDDT ATGGGATTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCAGAGGACTTCGATCCGGCGGACCCCTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACATTGTGCGTGAGAAGTGGGTGGCCATTGAGCGTGCCAAGATTTTGCGGGAGCGTGTGCGCCAATGCTACCGTCGCGAGGGCGTTAACCACCTTCAGAACTGCCGTACCTCTGTTCGCCAGTACCTGGAATCTCTCAAGGGCGTTGGCTGGGGCAAGGACGGCCGCCCTGCCTATGCCCACGACCCTGAATCCACCTGGCCTGCTACCCCTCC---------------------------------------------------------------------------- Asplenium_nidus_PSKY ATGGGCTTCAAG---GGC---GTGAAATTCGACGAGGTGCCTCCTGACGACTTCGATCCGGCGGACCCTTACAAGGACCCGGTGGCCTTCCTGGAGATGCGAGAGCACATCGTGCGTGAGAAGTGGGTAGCCATTGAGCGTTCGAAGATCTTGCGCGAGCGGGTACGGCAGTGCTACCGCCGTGAGGGTGTCAATCATCTTCAGAATTGCCGCACA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Asplenium_platyneuron_KJZG ATGGGCTTCAAG---GGC---GTGAAATTCGACGAGGCGCCTCCTGACGACTTCGACCCGGCAGACCCTTACAAGGACCCAGTGGCCTTCCTGGAGATGCGAGAGCACATCGTGCGCGAGAAGTGGGTAGCCATTGAGCGTGCAAAGATCTTGCGTGAGCGTGTGCGTCAGTGCTACCGCCGTGAGGGTGTCAATCATCTTCAGAATTGCCGCACAGCTGTGCGCCAGTATCTGGAATCTCTCAAGGGCATCGGGTGGGGCAAGGACGGCCGGCCCGCCTACGCACATGACCCTCTTTCCACTTGGCCTGCAACACCGCCCCCACCCCCCCCTTTCAAAGCTTCCTCTTGA--------------------------------------------- Athyrium_filixfemina_URCP ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGAAGACTTCGATCCGGCGGATCCTTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCAATCGCGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCTCGGCAGTGCGGCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGG---------------------------------------------------------------------------------------------------------------------------------------- Athyrium_sp_AFPO ---------------GGC---GTGAAATTTGACGAGGCGCCGCCTGAAGACTTCGATCCGGCTGATCCTTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCAATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCTCGGCAGTGCGCCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGGGCCGCCCCTCCTATGCCCACGATCCTCTTTCCACTTGGCCTGCAACACCGCCCCCGCCCCCCCCTTAA------------------------------------------------------------ Azolla_caroliniana_cf_CVEG ---------------------------------------------------------------------------------------------------------------------------TGGGTAGCGATCGAGAGGTCCAAGATCCTCCGGGAACGCGTCCGCAGGTGCTACCGCGAAGAAGGCGTGAACCACCTCCAGAATTGCCGGGTCGCGGTCCGCCGCTACCTCGAGTCCCTCAAAGGCGTGGGATGGGGTAAGGAAGGAAGGCCTGCATATGCCCATGATCCC------------------------------------------------------------------------------------------------------ Blechnum_spicant_VITX ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGAAGACTTCGATCCGGCGGATCCTTACAAGGACCCGGTGGCGTTCCTGGAAATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCTATCGAGCGCGCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCACAGCAGTGCACCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGGGCCGCCCCTCCTATGCCCACGACCCTCTTTCCACTTGGCCTGCAACACCGCCGCCGCCCCCCCCTTAA------------------------------------------------------------ Bolbitis_repanda_JBLI ATGGGATTCAAG---GGC---GTGAAGTTTGACGAGGCGCCTCCAGAGGACTTCGATCCGGCGGATCCGTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATTGAGCGGGCCAAGATTTTGCGCGAGCGCGTGAGCCAGTGCTATCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGTTCAGCGGTGCGCCAGTACTTGGAATCTCTCAAGGGCGTGGGGTGGGGCAACGAGGGCCGCCCCGCCTACGCCAACGACCCTCTCTCCACTTGGCCTGCCA??---------CCGCCCCCTTTCAAAGCTTCCTCTTAA--------------------------------------------- Botrypus_virginianus_BEGM ATGGTATTCAAA---GGTGAAGTCAAGTTTGATGAGACTCCCCCAGATGATTTTGACCCCGAGAACCCCTACAACGACCCCGTCGCGTTTTTCGAACAGCGAGAATATGTCGTCCGAGAGAAGCTCGTGGCCATCGAGACTGCCAAGATTCTCAGGGAAAGGGTGAGACAATGCTACTGGCTGGAGGGAGTGAATCACCATGAAAAGTGCAGGAAGGTGGTGCGGCAGTATCTGGATGCGATCAAGGGAGAGTGGGATGGGGCAAGGAATCGCGCCCCAAATTTGCGA---------------------------------------------CCGAGGTATCCAGATCCGAATAATTACAGTTTACACCCTCTCTTGGCTAGTTTCCTATACTCG Crepidomanes_venosum_TWFZ -------------------------------------------------------ATCCAGAGAATCCCTACAAGGATCCGGTCGCATACTTGGAGATGCGCGAACATTTGGTTCGGGAAAGGTGGATTGCCGTCGAGAAATCCAAAATACTCCGTGAGCGTGTACAGAAGTGCTACCGTCGGGAGGGCG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Cryptomeria_japonica_DSXO ATGGTTTTCAAG---GGCGAAGTTGAATTTGACGAAGGCCCACCTGACAATTTCGATCCAAAAAATCCATACGCAGATCCAGTGGCATTTTTTGAGTACAGAGAATACCTCGTGCGTGAGAAATGGATAGGCATTGAGACAGCCAAGATTCTGAGGGATAAAGTGAGATGGTGTTACAGGAAGGAAGGCGTCAATCATCTCCAGAATTGCAGAGAGATTGTTCGTCAATATCTCGAGTCCACCAAGGGCATCGGCTGGGGGAAAGACGCTCGCCCTCCTTATGCCCAC---------------------------------------------GGCACCGATACTGCTAAACCCTGA--------------------------------------- Culcita_macrocarpa_PNZO ATGGGGTTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCAGACGATTTCGATCCGGCGGATCCGTACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACTTGGTGCGGGAGAAGTGGGTGGCTATCGAGCGCGCCAAGATCCTACGGGAGCGCGTCCAGCAGTGCTACCGCCGGGAGGGTGTGAACCACCTTCAGAACTGCCGCACCACCGTCCGCCAGTATCTGGAATCCCTCAAGGGCGTCGGTTGGGGCAAGGAGGGCCGCCCCTCCTACGCCCACGATCCCAAATCCACCTGGCCCGCTACGCCGCCTCCGCCGCTGCCCTAAGTAAGGGCATATTAA--------------------------------------------- Cystopteris_fragilis_LHLE ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGACCCGGCGGATCCATACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACGTAGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGTGAGGGCGTCAACCACCTTCAGAACTGCCGCACAGCAGTGCACCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGG-------------------------------------------------------------------------------------------------------------------------------- Cystopteris_protrusa_YOWV ATGGGATTCAAG---GGC---GTGAAATTTGACGAAGCGCCGCCTGACGACTTCGACCCGGCGGATCCATACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACGTAGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGCTCAGCAGTGCACCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGG-------------------------------------------------------------------------------------------------------------------------------- Cystopteris_reevesiana_RICC ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGACCCGGCGGATCCATACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACGTAGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGCACAGCAGTGCACCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGG-------------------------------------------------------------------------------------------------------------------------------- Cystopteris_sp_XXHP ATGGGATTCAAG---GGC---GTGAAATTTGACGAAGCGCCGCCTGACGACTTCGACCCGGCGGATCCATACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACGTAGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGCTCAGCAGTGCACCAGTACTTGGAAT-------------------------------------------------------------------------------------------------------------------------------------------------------------- Cystopteris_utahensis_HNDZ ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCGGATCCATACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACGTAGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGCTCAGCAGTGCGCCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGGGCCGCCCCTCCTATGCCCACGACCCTCTTTCCACTTGGCCTGCAACACCGCCTCCGCCCCCCCCTTTCAAAGCTTCCTCTTAA--------------------------------------------- Davallia_fejeensis_OQWW ------TTCAAA---GGC---GTGAAGTTCGACGAGGCTCCGCCTGAGGACTTCGACCCGGCGGATCCGTACAAAGACCCGGTGGCGTTTCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCGTCGAGCGCGCCAAGATCTTGCGCGAGCGTGTGCGGCAGTGCTACCGGCGCGAGGGCGTCAACCACTTGCAGAACTGCCGCGTAGCAGTGCGTCAGTACTTGGAATCCCTCAAAGGCGTGGGGTGGGGCAAGGACACCCGCCCCGCCTATGCTCAAGACCCCAATTCCACTTGGCCTGCAACGCCGCCCCCTCCGCCCCCCTCTTGA--------------------------------------------------------- Dennstaedtia_davallioides_MTGC ATGGGATTCAAG---GGC---GTAAAGTTCGACGAAGCGCCGCCCGACGACTTCGATCCAGCGGATCCCTACAAGGACCCGGTAGCGTTCCTGGAGATGCGAGAGTACGTAGTGCGCGAGAAGTGGGTTGCTATCGAGCGCGCCAAGATCTTGCGTGAGCGTGTACGCCAATGCTACCGCCGCGAGGGCGTCAATCACCTCCAGAACTGCCGCTCCACAGTTCGCCAGTACATGGACTCCCTCAAAGGTGTGGGCTGGGGCAAGGAGGGCCGCCCCTCCTATGCCCACGACCCTCAATCC------------------------------------------------------------------------------------------------ Deparia_lobatocrenata_FCHS ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCACCTGACGACTTCGATCCGGCGGATCCTTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCTCAGCAGTGCGCCAGTACTTGGAATCCCTCAAGGGCGTCGGGTGGGGCAAGGAGGGCCGCCCCTCCTATGCCCACGACCCTCTTT-------------------------------------------------------------------------------------------------- Didymochlaena_truncatula_RFRB ATGGGATTCAAG---GGT---GTGAAATTTGACGAGGCGCCGCCCGACGACTTCGATCCGGCAGATCCATACAAGGACCCGGTGGCGTTCTTGGAAATGCGAGAGCATGTGGTGCGCGAGAAGTGGGTGGGCATCGAGCGCGCCAAGATCTTGCGCGAGCGCGTCCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAATTGCCGCTCAGCAGTGCGCCAGTACCTGGAATCCCTCAAGGGCGTGGGGTGGGGC--------------------------------------------------------------------------------------------------------------------------------------- Diplazium_wichurae_UFJN ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGAAGACTTCGATCCGGCGGATCCTTACAAGGACCCAGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGAGAGCGTGTGCGGCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCTCGGCAGTACGCCAGTACTTGGAATCTCTCAAGGGCGTGGGGTGGGGCAAGGAGG-------------------------------------------------------------------------------------------------------------------------------- Dipteris_conjugata_MEKP ATGGTTTTCAAG---GGC---GTGAAGTTCGATGAGACTCCTCCCGATGATTTCGATCCGGCTCAGCCCTACAAGGACCCCGTCGCCTTTCTGGAGATGCGCGAGTACTTGGCTCGGGAAAAATGGGTTGCCATCGAGAAGTCCAAAATCCTCCGTGAACGAGTGCAGAAATGCTACCGACTGGAGGGCGTTAATCACCTCCAAAACTGCCGGAAGGTCGTCCGCCTGTACCTCGCCTCTCTTAAAGACGTTGGATGGGGCAAGGATGTCCGTCCTGAATACGCAAAC---------------------------------------------AATGTTTCTCCGTGA------------------------------------------------ Encephalartos_barteri_GNQG ATGGTTTTCAAG---GGCGAAGTTGAATTTGATGAAGGCCCCCCTGATGATTTTGATCCCAAAAATCCATATGCAGATCCAGTGGCAATGCTGGAGCAGCGGGAATATCTTGTACGAGAGAAATGGATTCAGATAGAGACTGCTAAAATTCTGAAGGAGAAGGTGAAGTGGTGTTACCGGAGAGAAGGCGTTAACCATCTTCAGAAATGCAGAGCTATTGTTCGACAGTACCTTGATTCTACCAGGGGAATTGGGTGGGGCAAGGATACTCGACACCATTTATTTCAA---------------------------------------------GGTGGCCCGACTAAATCTGTTGAATTTTCCCATAACTGA------------------------ Equisetum_diffusum_CAPN ATGGTGTTCAAG---GGGGAGGTGAAGTTCGACGATGCACCGCCGGAGGATTTCGACCCGAGCGACCCTTACAAGGACCCCGTGGCCTTCCTCGAGATGAGGGAGTACATAACCAGGGAGAAGCTCATAGGCGTGGAGCGCGCCAAGATCCTCCGCGAGCGTGCGCGCCGCTGCTATCGCCGTGAGGGCGTAAACCACTACCAGAACTGCCGCCAAATCGTGCGTCAATACCTTGATTCCATCAAAAACGTCGGATGGGGCAACGAATATCGCCCTGACTATCCACTC---------------------------------------------AG------------------------------------------------------------- Equisetum_hyemale_JVSZ ATGGTGTTCAAG---GGGGAGGTGAAGTTCGACGATGCACCGCCGGAGGATTTCGACCCCAGCGACCCTTACAAGGATCCCGTGGCCTTTCTCGAGATGAGGGAATACATAACCAGGGAGAAGCTCATAGGGGTGGAGCGCGCTAAGATCCTGCGCGAGCGCGCGCGCCGTTGCTATCGCCGCGAGGGTGTAAATCACTACCAGAACTGCCGCGAAATCGTGCGCCAATACCTTGAATCCATAAAAAATGTAGGATGGGGCAATGAATATCGCCCTTACTA------------------------------------------------------------------------------------------------------------------- Gaga_arizonica_DCDT ATGGGATTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCAGAGGACTTCGATCCGGCGGACCCCTACAAGGACCCGGTGGCGTTCCTGGAAATGCGAGAGCACATTGTGCGCGAGAAGTGGGTGGCCATTGAGCGTGCCAAGATCTTGCGCGAGCGTGTGCGCCAATGCTACCGTCGTGAGGGCGTTAACCACCTCCAGAACTGCCGTACCGCTGTTCGTCAGTACCTGGAATCTCTCAAGGGCATTGGCTGGGGCAAGGATGGCCGCCCTGCGTATGCCCACGATCCTCAATCCACCTGGCCTGCTACCCCACCTCCACCTCCGCCCTTCAAGTAG------------------------------------------------------ Gymnocarpium_dryopteris_HEGQ ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCGGATCCGTACAAGGACCCGGTGGCGTTTCTGGAGATGCGGGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGTTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGCTCAGCAGTGCGCCAGTACTTGGAATCCCTCAAGGGCGTGGGG--------------------------------------------------------------------------------------------------------------------------------------------- Homalosorus_pycnocarpos_OCZL -------------------------AATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCGGATCCTTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCGCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCTCAGCAGTGCGGCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGGGCCGCCCCGCCTATGCCCACGACCCTCTTTCCACTTGGCCTGCAACACCGCCCCCACCCCCTCCTTCTTAA--------------------------------------------------------- Hymenophyllum_bivalve_QIAD ATGGGATTCAAG---GGC---GTCAAGTTCGATGAGACACCTCCGGATGATTTCGATCCAGAGAATCCCTACAAGGATCCGGTAGCGTTCTTGGAGATGCGCGAGCATTTGGTTAGGGAAAAATGGATTGCTATCGAGAAATCCAAAATCCTCCGTGAGCGTGTACAGAAGTGCTACCGACGCGAGGGCGTGAACCACCTCCAGAACTGCCGGAAGATCGTGCGCCAGTATCTCGGTTCTTTGAAAGATGCTGGTTGGGGCAAAGAGTCCCGCCCTGCCTACACAAAT---------------------------------------------TTCTGA--------------------------------------------------------- Hymenophyllum_cupressiforme_TRPJ ATGGGATTCAAG---GGC---GTCAAGTTCGATGAGACACCTCCGGATGATTTCGATCCAGAGAATCCCCACAAGGATCCGGTAGCGTTCTTGGAGATGCGCGAGCATTTGGTTCGGGAAAAATGGATTGCTATCGAGAAATCCAAAATCCTCCGTGAGCGTGTACAGAAGTGCTACCGTCGCGAGGGCGTGAACCACCTCCAGAACTGCCGGAAGATCGTGCGCCAGTATCTCGGTTCTTTGAAAGATGCTGGCTGGGGCAAAGAGTCCCGCCCTGCCTACACAAAT---------------------------------------------TTCTGA--------------------------------------------------------- Leucostegia_immersa_WGTU ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCAGCGGATCCTTACAAAGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTAGTGCGGGAGAAGTGGGTGGCGATCGAGCGCGCCAAGATCTTGCGCGAGCGTGTGCGCCAGTGCTACCGCCGGGAGGGGGTCAACCACCTTCAGAACTGCCGCTTAGCAGTGCGCCAGTACCTGGAGTCCCTCAAGGGCGTGGGGTGGGGAAAGGAGGGCCGACCCTCCTACGCCCACGACCCTCTTTCCACTTGGCCTGCAACTCCGCCCCCGCCCCCCCCTTTCAAAGCTTCCTCCTAA--------------------------------------------- Lindsaea_linearis_NOKI ATGGGGTTCAAA---GGC---GTGAAGTTCGACGAGACGCCACCGGACGATTTCGATCCTGCGGATCCTTACAAGGATCCCGTGGCCTTCTTGGAGATGCGAGAGCACATTGTGCGCGAGAAGTGGGTCGACATCGAGCGCGCCAAGATTCTGCGTGAGCGCGTCCGACAGTGCTACAAACGTGAGGGCGTCAATCACCTCCAGAACTGCCGCATTGCAGTGAGGAAGTATCTCGAATCCCTCAAAGGCGTCGGGTGGGGCAAAGACGGCCGCCCTGCATACGCTCATGATCCCGAGTCCACTTGGCCTGCCACACCGCCTGCACCGCCGGCATTCAAGCGTTAG--------------------------------------------------- Lindsaea_microphylla_YIXP ATGGGGTTCAAA---GGC---GTGAAGTTCGACGAGACGCCACCGGACGACTTCGATCCTGCGGATCCCTACAAGGATCCCGTGGCCTTCTTGGAGATGCGAGAGCACATTGTGCGCGAGAAGTGGGTCGACATCGAGCGCGCCAAGATCCTGCGTGAGCGCGTCCGACAGTGCTACAAACGTGAGGGCGTCAATCACCTCCAGAACTGCCGCATTGCAGTGAGGAAGTATCTCGAATCCCTCAAAGGCGTCGGGTGGGGCAAAGACGGCCGCCCTGCATACGCTCATGATCCCGAGTCCACTTGGCCTGCCACACCGCCTGCACCACCGGCATTCAAGCGTTAG--------------------------------------------------- Lygodium_japonicum_PBUU ATGGGATTCAAG---GGC---GTGAAGTTTGACGAGGGCCCTCCAGAGGATTTCGACCCGCAGGATCCCCACAAGGACCCCGTGGCCTACCTGGAGATGCGCGAGTATGTGGTCCGCGAGAAGTGGGTCGCCATCGAGAAGGCCAAGATCCTGCGCGAGCGCGTCCGGCAGTGCTACCGCCGCGAGGGCGTGAACCACCTCCAGAACTGCCGCAAGCAGGTGCGCCAGTACCTCGCCTCCCTCAACAATGTTGGCTGGGGCAAGGACGTGCGCCCCGCGTACGCCAAC---------------------------------------------AACTTCAAGGAATGA------------------------------------------------ Myriopteris_rufa_GSXD ATGGTATTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCAGAGGACTTCGATCCGGCGGACCCCTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACATTGTGCGCGAGAAGTGGGTGGCCATCGAGCGTGCCAAGATCTTTCGCGAGCGTGTGCGCCAATGCTACCGCCGCGAGGGCGTTAACCACCTTCAGAACTGCCGTACAGTTGTTCGCCAGTATCTGGAATCTCTTAAGGGCGTTGGCTGGGGCAAGGATGGCCGCCCTGCCTATGCCCACGACCCTCAATCCACCTGGCCTGCTACCCCACCTCCACCTCCTCCCTTCAAGTGA------------------------------------------------------ Nephrolepis_exaltata_NWWI -------------------------------------------------------------------CGTACAAGGATCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCGCCAAGATCTTGCGGGAGCGCGTGCGCCAGTGCTACCGTCGTGAGGGCGTCAACCATCTTCAGAACTGCCGCAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Notholaena_montieliae_YCKE ATGGGATTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCTGAGGACTTTGATCCGGCGGACCCCTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACATTGTGCGAGAGAAGTGGGTGGCCATTGAGCGTGCCAAGATCTTGCGAGAGCGTGTGCGCCAATGCTACCGCCGTGAGGGTGTTAATCACCTTCAGAACTGCCGTACCGCTGTTCGCCAGTACCTGGAATCTCTCAAGGGAATTGGCTGGGGCAAGGATGGTCGCCCTGCCTATGCACACG----------------------------------------------------------------------------------------------------------- Onoclea_sensibilis_HTFH ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCGGATCCTTACAAGGACCCGGTGGCGTTCCTGGAGATGAGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGCGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGCTCAGCCGTGCGCCAGTACTTGGAATCCCTCAAGGGTGTCGGGTGGGGCAAGGAGGGCCGCCCCTCCTATGCCCACGACCCTCTTTCCACTTGGCCTGCAACACCGCCCCCGCCCCCCCCTTAA------------------------------------------------------------ Ophioglossum_sp_QHVS ATGGTGTTCAAA---GGTGAGGTGAAGTTCGATGATAGCCCACCAGAAGATTTCGATCCTGAGAACCCATATAAAGACCCCGTCGCCTTCTTGGAGCAGAGGGAGTATGTGACCAGAGAGAAGCTGATTGCCATCGAGACTTCCAAGATTCTGAAGGAAAGGGTTCGTCAGTGCTACTGGCTGGAGGGTGTCAACCACCTAGAGAAGTGCAGAAAAGTCGTTCGTCAGTATCTGGACTCACTTAAGGATGTAGGATGGGGCAAAGAATCACGACCTAAATTTACAACC---------------------------------------------CAGGTTTCTGGATCTGAATAA------------------------------------------ Osmunda_sp_UOMY ATGGTGTTCAAG---GGCGAGGTGAAGTTCGATGAGACTCCGCCTGATGATTTCGATCCGGAGCACCCCTACAAGGACCCCGTCGCCTTCCTGGAGATGCGGGAACACATTGCTCGTGAAAAGTGGGTTGCCGTGGAGAAATCTAAAATCCTCCGGGAAAGAGTCCAGCAATGTTACCGACGGGAGGGCGTGAATCACCACCAGAACTGTAGGAAGATCGTGCGCCTGTACCTTGATTCGATCAAAAATGTTGGATGGGGCAAGGAAGCTCGTCCGGCCTACACAAAT---------------------------------------------CTCTAG--------------------------------------------------------- Parahemionitis_cordata_ZXJO ATGGGATTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCAGAGGACTTCGATCCGGAGGACCCCTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACATTGTGCGCGAGAAGTGGGTGGCCATTGAGCGTGCTAAGATCTTGCGCGAGCGTGTGCGCCAATGTTACCGTCGTGAGGGCG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Peperomia_fraseri_XSZI ATGGTGAGGAAGGCGAAG---GTGGAGTTCGACGAGGGCCCGCCGGACAACTTCGATCCGGCGAACCCGTACGCCGACCCGGTGGCGATGCTGGAGATGCGGGAGTACCTTGTGAGGGAGAAGTGGATCCAGATCGAGACGGCCAAGATTTTGCGTGAAAGGGTACAGCGGTGCTACCGCGTCGAAGGGGTCAACCACCGGCAGAAATGCCGCGAGATCGTCCAGCAGTACCTCGACGCCACCCGCGGCGTCGGCTGGGGCAAGGACAACCGTCCCCACGTGCTCCACGGTCCGAAG------------------------------------GTTGAAGCGGCTGAGTAGAGCGGTCAATTGA-------------------------------- Phlebodium_pseudoaureum_ZQYU ATGGGATTCAAA---GGC---GTGAAGTTCGACGAAGCCCCGCCTGACGACTTCGACCCGGCGGATCCGTACAAGGACCCGGTGGCGTTTCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATTGAGCGCGCCAAGATCTTGCGCGAGCGTGTGCGGCAGTGCTACCGGCGCGAGGGCGTTAACCACCTCCAGAACTGCCGGGTGGCAGTGCGTCAGTACTTGGAGTCCATCAAAGGCGTGGGGTGGGGCAAGGACAGCCGCCCCGCCTATGCTCATGACCCCAATTCTACTTGGCCTGCAACACCGCCCCCTCCGCCCCCCTCTTAA--------------------------------------------------------- Phymatosorus_grossus_ORJE ATGGGATTCAAA---GGC---GTGAAGTTCGACGAATCTCCGCCTGAAGACTTCGACCCGGCGGATCCATACAAGGACCCGGTGGCGTTCTTGGAGATGCGAGAGCACGTGGTTCGCGAGAAGTGGGTGGCCATCGAGCGTGCCAAGATCTTGCGCGAGCGTGTGCGGCAGTGCTACCGGCGCGAGGGCGTCAACCATCTCCAGAATTGCCGGGTGGCAGTACGACAGTACCTGGAATCCATCAAAGGCGTGG??---------------------------------?ACCCCAATTCCACTTGGCCCGCAACACCGCCCCCTCCGCCTCCATCTTAA--------------------------------------------------------- Pilularia_globulifera_KIIX ATGGGTTTCAAG---GGC---GTGAAGTTCGACGAATCGCCGCCGGACGATTTCGACCCGGCGGATCCGTACAAGGATCCGGTGGCGTTCCTGGAGATGCGGGAGCACGTCGTACGGGAGAAATGGGTGGCCATCGAGCGATCTAAGATCCTGCGGGAGCGCGTTCGCCAGTGCTACCACCGCGAGGGAGTGAACCACCTCCAGAATTGCCGTACTGCGGTCCGCCAATACCTGGAATCCCTCAAAGGCGTTGGCTGGGGCAAAGAGGGCCGCCCTGCCTACGCCCATGACCCTCAGTCCACGTGGCCTGCCACACCGCCACCGCCTCCGCCTTCCGCTCGCTCTTCGTAG--------------------------------------------- Pityrogramma_trifoliata_UJTT ATGGTGTTCAAG---GGC---GTGAAGTTCGACGAGGCGCCGCCGGAGGATTTTGATCCGGCGGATCCATACAAGGACCCGGTGGCGTTTCTGGAGATGCGAGAGCATATCGTGCGCGAGAAGTGGGTCTCCATTGAGAGAGCCAAGATCATGCGGGAGCGTGTGCGTCAGTG?---------GAAGGCGTTAATCACCTCCAGAATTGCCGCATTGCTGTTCGCCGCTACCTTGAATCCCTGAAAGGCGTTGGCTGGGGCAAGGATGGCCGCCCTTCGTACGCCCATGACCCCAGTTCCACCTGGCCTGCCACCCCACCCCCTCCACCTCCCTTCAAGTAA------------------------------------------------------ Plagiogyria_japonica_UWOD ATGGGTTTCAAG---GGA---GTGAAGTTCGACGAGGCGCCGCCGGACGATTTCGATCCGGCGGATCCGTACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACTTGGTGCGAGAGAAGTGGGTGGCCATCGAGCGGGCCAAGATCTTGCGGGAGCGAGTCCAGCAGTGCTACCGCCGGGAGGGTGTGAACCACCTTCAGAACTGCCGCACCACCGTCCGCCAGTATCTGGAATCCCTCAAGGGCGTCGGCTGGGGCAAGGAGGGCCGCCCCTCCTACGCCCACGATCCCAAATCCACCTGGCCCGCTACGCCGCCTCCGCCACTGCCATCTTAA--------------------------------------------------------- Pleopeltis_polypodioides_UJWU ATGGGATTCAAA---GGC---GTGAAGTTCGACGAAGCCCCGCCTGAGGACTTCGACCCGGCGGATCCGTACAAGGACCCGGTGGCGTTTCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCGCCAAGATCTTGCGCGAGCGTGTGCGGCAGTGCTACCGGCGCGAGGGCGTCAACCACCTCCAGAACTGCCGCGTGGCGGTGCGTCAGTACTTGGAATCCATCAAAGGCGTGGGGTGGGGCAAGGACAGCCGCCCCGCCTACGCTCATGACCCCAATTCCACTTGGCCTGCAACACCGCCCCCTCCGCCCCGCTTCTAA--------------------------------------------------------- Polypodium_amorphum_YLJA ATGGGATTCAAA---GGC---GTGAAGTTCGACGAAGCCCCGCCTGACGACTTCGACCCGGCGGATCCGTACAAGGACCCGGTGGCGTTTCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATTGAGCGCGCCAAGATTTTGCGCGAGCGTGTGCGGCAGTGCTACAGGCGCGAGGGCGTCAACCACCTCCAGAACTGCCGGGTGGCAGTGCGTCAGTACTTGGAATCCATCAAAGGCGTGGGGTGGGGCAAGG----------------------------------------------------------------------------------------------------------------------------------- Polypodium_glycyrrhiza_CJNT -------------------------AGTTCGACGAAGCCCCGCCTGACGACTTCGACCCGGCGGATCCGTACAAGGACCCGGTGGCGTTTCTGGAGATGCGAGAGCATGTGGTGCGCGAGAAGTGGGTGGCCATTGAGCGCGCCAAGATTTTGCGGGAGCGTGTGCGGCAGTGCTACCGGCGCGAGGGCGTCAACCACCTCCAGAACTGCCGGGTGGCAGTGCGTCAGTACTTGGAATCCATCAAAGGCGTGGGGTGGGGCAAGGACACCCGCCCCGCCTATGCTCATGACCCCAATTCCACTTGGCCTGCAACACCGCCCCCTCCGCCCCCCTCTTAA--------------------------------------------------------- Polypodium_hesperium_B_IXLH ATGGGATTCAAA---GGC---GTGAAGTTCGACGAAGCCCCGCCTGACGACTTCGACCCGGCGGATCCGTACAAGGACCCAGTGGCGTTTCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATTGAGCGCGCCAAGATTTTGCGGGAGCGTGTGCGGCAGTGCTACCGGCGCGAGGGCGTCAACCACCTCCAGAACTGCCGGGTGGCAGTGCGTCAGTACTTGGAATCCATCAAAGGCGTGGGGTGGGGCAAGGACCCCCGCCCCGCCTATGCTCATGACCC------------------------------------------------------------------------------------------------------- Polypodium_hesperium_GYFU ATGGGATTCAAA---GGC---GTGAAGTTCGACGAAGCCCCGCCTGACGACTTCGACCCGGCGGATCCGTACAAGGACCCAGTGGCGTTTCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATTGAGCGCGCCAAGATTTTGCGGGAGCGTGTGCGGCAGTGCTACCGGCGCGAGGGCGTCAACCACCTCCAGAACTGCCGGGTGGCAGTGCGTCAGTACTTGGAATCCATCAAAGGCGTGGGGTGGGGCAAGGAC--------------------------------------------------------------------------------------------------------------------------------- Polystichum_acrostichoides_FQGQ ATGGGTTTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCGGATCCTTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCGCCAAGATCTTGCGCGAGCGCGTGAACCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGCCGCTCAGCAGTGCGCCAGTACTTGGAATCCCTCAAAGGCGTGGGGTGGGGCAAGGAGGGCCGCCCCTCCTATGCCCACGACCCTCTTTCCACTTGGCCTGCAACACCGCCCCCGCCCCCCCCTTTCAAAGCTTCCTCTTAA--------------------------------------------- Psilotum_nudum_QVMR ATGGTGTTCAAA---GGAGAAGTGAAGTTCGATGATGCTCCCCCTGAGGATTTTGATCCCCAAGATCCTCACAAGGATCCCATTGCATTCTTGGAGCAGCGAGAATACATCGTGCGACAGAAGCTTGTGGCCATCGAGACTGCTAAGATTCTCAGGGAGCGTGTGGCGCACTGCTATTTTCTGGAGGGAGTGAACCATTACCAGAACTGCAAGAAGGTGGTGCGTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pteridium_aquilinum_Pt_Contig4243 ATGGGATTCAAG---GGC---GTGAAGTTCGACGAGTCGCCGCCGGACGACTTCGATCCAGCGGATCCCTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTAGTGCGCGAGAAGTGGGTGGCTATCGAGCGCTCCAAGATCCTGCGTGAGCGTGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTCCAGAACTGCCGCTCCGCCGTTCGCCAGTACCTGGAATCCCTCAAAGGCGTGGGCTGGGGCAAGGATGGCCGCCCTTCATACGCCCACGACCCTCAATCCACTTGGCCTGCAACACCGCCCCCTCCCCCCCCTTTCAAAGCTTCCTAA------------------------------------------------ Pteris_ensiformis_FLTD ATGGTATTCAAG---GGC---GTGAAATTCGACGAGGCGCCGCCGGAAGACTTTGATCCGGCGGATCCGTACAAGGATCCGGTGGCGTTCCTGGAGATGCGAGAGCATATAGTGCGCGAGAAGTGGGTGGCCATCGAGCGAGCCAAGATCTTCCGGGAGCGTGTGCGACAATGCTACCGTCGGGAAAGCGTAAACCACCTCCAAAATTGCCGTCCTGCTGTTCGGAAGTACCTAGAATCTCTCAAAGGCGTTGGCTGGGGCAAGGAGGGCCGCCCTGCTTATGCCCACGACCCTCAATCCACGTGGCCTGCTACCCCACCCCCGCCTCCTCCCTTCAAGTAGGT---------------------------------------------------- Pteris_vittata_POPJ ATGGTATTCAAG---GGC---GTCAAGTTCGACGAGGCGCCGCCAGAAGACTTTGATCCGGCGGATCCGTACAAGGACCCAGTGGCGTTCCTGGAGATGCGGGAACACATAGTGCGCGAGAAGTGGGTGCAAATCGAGCGAGCCAAGATTAAACGGGAGCGTGTGCGACAATGCTACCGCCGGGAAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sceptridium_dissectum_EEAQ ATGGTGTTCAAA---GGTGATGTCAAGTTTGATGAGACTCCCCCAGATGATTTTGACCCGGAGAACCCCTACAACGACCCCGTCGCATTTTTGGAACAGCGAGAATATGTCGTCCGAGAGAAGCTTGTGGCCATTGAGACTGCCAAGATTCTTAGGGAAAGGGTGAGGCAATGCTACTGGCTGGAGGGAGTGAATCACCATGAAAAGTGCAGGAAGGTGGTGCGCCAGTATTTGGATGCGATAAAGGGAGTGGGATGGGGCAAGGAATCACGCCCCAAATTTGCAACC---------------------------------------------GAGGTATCTAGATCTGAATAA------------------------------------------ Sticherus_lobatus_XDVM ATGGGTTTCAAG---GGC---GTGAAGTTTGATGAGACCCCTCCTGATGATTTCGATCCAGAGCACCCTTACAAGGACCCTGTCGCATTTCTGGAGATGCGCGAACACATCGTCCGCGAAAAGTGGATCGCCATCGAGACCTCTAAAATCCTCCGTGAGCGCGTCCAGAAGTGCTACCGCGAGGAGGGCGTGAATCACCTCCAGAGCTGCCGGAAGATCGTGCGTCAGTACCTTTCCTCGCTTCGGAACGTTGGATGGGGCAAGGATGCCCGTCCTGCCTACTGTGAC---------------------------------------------ACGCTCTGA------------------------------------------------------ Thelypteris_acuminata_MROH ATGGGATTCAAA---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCTGATCCTTACAAGGACCCGGTGGCATTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCGCCAAGATCTTGCGTGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAATCACCTTCAGAACTGTCGCTCAGCAGTGCGTCAGTACTTGGAATCCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------- Thyrsopteris_elegans_EWXK ATGGGCTTCAAG---GGC---GTGAAGTTCGACGAAGCGCCGCCAGACGATTTCGATCCGGCGGATCCATACAAGGACCCCGTGGCATTCCTGGAGATGCGGGAGCACGTGGTGCGGGAGAAGTGGGTGGCCATCGAGCGCGCCAAGATCCTGCGGGAGCGCGTCCAGCATTGCTACCGCCGGGAGGGAGTAAACCACCTCCAGAACTGCCGCACCGCCGTCCGCCAGTACCTGGAATCCCTCAAGGGCGTTGGCTGGGGCAAGGAGGGCCGCCCCGCCTATGCCCACGACCCCGAATCAACCTGGCCCGCCACGCCGCCTCCGCCGCGGCCCTCCGCAAGGACATCTTAA--------------------------------------------- Tmesipteris_parva_ALVQ ATGGTGTTCAAA---GGAGAAGTGAAGTTCGATGACGCTCCGCCTGAGGATTTTGATCCTCAAAACCCTCACAAGGATCCGATTGCATACTTGGAGCAGCGAGAATACATCGTGCGACAGAAGCTTGTGGCCATCGAGACAGCCAAGATTCTCAGGGAGCGCGTGGCGCGGTGCTATTTTCTGGAGGGAGTGAACCATTACCAGAATTGTAAGAAGGTGGTGCGTCAGTATCTTGATTCGATCAAGGGGTTGGGATGGGGCGTTGAG------------------------------------------------------------------CGTCCTGATATTTGA------------------------------------------------ Vittaria_appalachiana_NDUV ATGGGATTCAAA---GGC---GTGCACTTCGACGAGAGGCCTCCAGAGGACTTCGATCCTGAAAACCCATACAAGGACCCTGTGGCGTTTCTGGAGATGCGAGAGCACATAGTGCGCGAGAAGTGGGTTTCAATAGAGCGAGCCAAGATCTTGCGCGAGCGTGTGAGCCAATGCTACCGCCGGGAGGGCGTTAATCACCTTCAGAACTGCCGCGTTGCCGTCCGTCAGTACTTGGAATCCCTCAAGGGCCTTGGCTGGGGCAACGATGGGCGCCCTGCCTATGCGCAGGACCCCAATTCTACCTGGCCCGCCACTCCCCCTCCGCCTCCTCCTTTCAAGAAGTAG--------------------------------------------------- Vittaria_lineata_SKYV ---------------??C---GTGCACTTCGACGAGAGGCCTCCAGAGGACTTCGATCCCGAAAACCCATACAAGGACCCTGTGGCGTTTCTGGAGATGCGAGAGCACATAGTGAGGGAGAAGTGGGTTTCAATCGAGCGAGCCAAGATCCTGCGCGAGCGTGTGCGCCAGTGCTACCGCCGAGAGGGCGTGAATCACCTTCAGAACTGTCGTGTTGCTGTCCGCCAGTACTTGGAATCCCTCAAGGGCCTTGGCTGGGGCAACGATGGGCGCCCTGCCTATGCGCAGGACCCCAATTCTACCTGGCCCGCCACTCCCCCTCCTCCTCCTCCTTTCAAGAAGTAG--------------------------------------------------- Woodsia_ilvensis_YQEC ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCGGATCCGTACAAGGACCCGGTGGCGTTCCTGGAGATGCGGGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGGGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCTCCGCAGTGCACCAGTACTTGGAATCCCTCAAGGGCATCGGGTGGGGCAAGGAGGGCCGCCCCTCCTACGCCCACGACCCTCTTTCCACTTGGCCTGCAACACCGCCCCCGCCCCCCCCTTTCAAAGCTTCTTCTTGA--------------------------------------------- Woodsia_scopulina_YJJY ATGGGATTCAAG---GGC---GTGAAATTTGACGAGGCGCCGCCTGACGACTTCGATCCGGCGGATCCGTACAAGGACCCGGTGGCGTTCCTGGAGATGCGAGAGCACGTGGTGCGCGAGAAGTGGGTGGCCATCGAGCGCTCCAAGATCTTGCGGGAGCGCGTGCGCCAGTGCTACCGCCGCGAGGGCGTCAACCACCTTCAGAACTGTCGCTCAGCAGTGCGCCAGTACTTGGAATCCCTCAAGGGCGTGGGGTGGGGCAAGGAGGGCCGCCCCTCCTACGCCCACGACCCTCTTTCCACTTGGCCTGCAACACCGCCCCCGCCCCCCCCTTTCAAAGCTTCTTCTTAA--------------------------------------------- Zea_mays_GRMZM2G173277_T02 ATGGTGCGCAAGGCGAAG---GTTGAGTTCGACGAGCAGCCGCCGGATAACTTCGACCCGAAGAACCCGTATGCCGACCCGGTGGCGATGCTCGAGTACCGGGAACACCTGGTGCGAGAGAAGTGGATCCATATCGAGACCGCCAAGATCATCCGGGAGCGCCTCCGCTGGTGCTACCGCATCGAGGGCATCAACCACCACCAGAAGTGCCGCCACCTCGTCGACCAATACCTAGAGGCTACCCGCGGCGTGGGTTGGGGCAAGGATGCCCGCCCGCCTGAACTCCACGAGCCCAAG------------------------------------AAGACCGTCAAGGCGGAGTAG------------------------------------------ ; END; BEGIN TREES; Title NDUFS6; LINK Taxa = Taxa; TRANSLATE 1 Adiantum_aleuticum_WCLG, 2 Adiantum_raddianum_BMJR, 3 Alsophila_spinulosa_GANB, 4 Amborella_trichopoda_scaffold00079.32, 5 Anemia_tomentosa_CQPW, 6 Angiopteris_evecta_NHCM, 7 Aquilegia_coerula_Aquca_00292.1, 8 Arabidopsis_thaliana_AT1G49140, 9 Argyrochosma_nivea_XDDT, 10 Asplenium_nidus_PSKY, 11 Asplenium_platyneuron_KJZG, 12 Athyrium_filixfemina_URCP, 13 Athyrium_sp_AFPO, 14 Azolla_caroliniana_cf_CVEG, 15 Blechnum_spicant_VITX, 16 Bolbitis_repanda_JBLI, 17 Botrypus_virginianus_BEGM, 18 Crepidomanes_venosum_TWFZ, 19 Cryptomeria_japonica_DSXO, 20 Culcita_macrocarpa_PNZO, 21 Cystopteris_fragilis_LHLE, 22 Cystopteris_protrusa_YOWV, 23 Cystopteris_reevesiana_RICC, 24 Cystopteris_sp_XXHP, 25 Cystopteris_utahensis_HNDZ, 26 Davallia_fejeensis_OQWW, 27 Dennstaedtia_davallioides_MTGC, 28 Deparia_lobatocrenata_FCHS, 29 Didymochlaena_truncatula_RFRB, 30 Diplazium_wichurae_UFJN, 31 Dipteris_conjugata_MEKP, 32 Encephalartos_barteri_GNQG, 33 Equisetum_diffusum_CAPN, 34 Equisetum_hyemale_JVSZ, 35 Gaga_arizonica_DCDT, 36 Gymnocarpium_dryopteris_HEGQ, 37 Homalosorus_pycnocarpos_OCZL, 38 Hymenophyllum_bivalve_QIAD, 39 Hymenophyllum_cupressiforme_TRPJ, 40 Leucostegia_immersa_WGTU, 41 Lindsaea_linearis_NOKI, 42 Lindsaea_microphylla_YIXP, 43 Lygodium_japonicum_PBUU, 44 Myriopteris_rufa_GSXD, 45 Nephrolepis_exaltata_NWWI, 46 Notholaena_montieliae_YCKE, 47 Onoclea_sensibilis_HTFH, 48 Ophioglossum_sp_QHVS, 49 Osmunda_sp_UOMY, 50 Parahemionitis_cordata_ZXJO, 51 Peperomia_fraseri_XSZI, 52 Phlebodium_pseudoaureum_ZQYU, 53 Phymatosorus_grossus_ORJE, 54 Pilularia_globulifera_KIIX, 55 Pityrogramma_trifoliata_UJTT, 56 Plagiogyria_japonica_UWOD, 57 Pleopeltis_polypodioides_UJWU, 58 Polypodium_amorphum_YLJA, 59 Polypodium_glycyrrhiza_CJNT, 60 Polypodium_hesperium_B_IXLH, 61 Polypodium_hesperium_GYFU, 62 Polystichum_acrostichoides_FQGQ, 63 Psilotum_nudum_QVMR, 64 Pteridium_aquilinum_Pt_Contig4243, 65 Pteris_ensiformis_FLTD, 66 Pteris_vittata_POPJ, 67 Sceptridium_dissectum_EEAQ, 68 Sticherus_lobatus_XDVM, 69 Thelypteris_acuminata_MROH, 70 Thyrsopteris_elegans_EWXK, 71 Tmesipteris_parva_ALVQ, 72 Vittaria_appalachiana_NDUV, 73 Vittaria_lineata_SKYV, 74 Woodsia_ilvensis_YQEC, 75 Woodsia_scopulina_YJJY, 76 Zea_mays_GRMZM2G173277_T02; TREE NDUFS6_bestREP2 = (5:0.18379484,(((41:0.00759715,42:0.00471458):0.20427501,((((27:0.0573605,(((29:0.05195428,(((((((36:0.01035353,(25:1.0E-8,((24:1.0E-8,22:1.0E-8):0.00431733,(23:1.0E-8,21:0.00439289):0.00453946):0.00897759):0.00782359):0.00897954,(75:1.0E-8,74:0.01755727):0.00716851):0.00327618,(28:0.0036131,47:0.01355484):0.00343652):1.0E-8,(30:0.02843345,(13:0.0042745,12:0.00945442):0.00417638):0.00851347):0.00328644,(37:0.01405871,(69:0.03564693,15:0.02068875):1.0E-8):1.0E-8):0.00335622,62:0.01343541):1.0E-8,((45:0.04758002,(26:0.03036711,((53:0.06921182,((((60:1.0E-8,61:1.0E-8):0.00794862,59:0.00340812):0.00518176,58:0.00459213):0.00496482,52:0.00996423):0.00602565):0.00489365,57:0.01017357):0.01046747):0.07437495):0.02672077,16:0.06650714):0.01926076):0.00434004):0.00720879,40:0.04480263):1.0E-8,(10:0.04985621,11:0.01301967):0.13078512):0.05318779):0.01113224,64:0.02766497):0.03976519,(((14:0.3494952,55:0.04286984):0.10660019,(65:0.04449045,66:0.10370997):0.02200823):0.04964666,(((2:0.06263977,9:0.01978062):0.0078903,((50:0.01118829,(73:0.03733843,72:0.00967037):0.20550602):0.00847565,(46:0.04090038,35:0.01764351):1.0E-8):0.00552228):0.0048493,(1:0.05213284,(44:1.0E-8,(33:1.0E-8,34:0.09042275):0.60330559):0.01377035):0.00961479):0.02221192):0.05051476):0.0325065,(54:0.12127171,(70:0.05223865,((56:0.03556718,20:0.01162708):0.03999556,3:0.08674801):0.00386448):0.07469089):0.0371998):0.04020585):0.15857305,(((39:0.00514315,38:0.00905971):0.04243126,18:0.0471382):0.11419621,(68:0.17207037,(31:0.12996546,((((((71:0.05748769,63:0.02066869):0.34382027,(17:0.19631156,67:0.01031687):0.06289808):0.09213355,48:0.23454681):0.22263712,6:0.26013414):0.07180057,((32:0.13310301,((8:0.35775356,7:0.08022409):0.15400399,(4:0.2220578,(76:0.36669064,51:0.25756307):0.18627197):0.15228857):0.26071443):0.11157083,19:0.1492197):0.52740134):0.13783043,49:0.10238167):0.07509554):0.04353027):0.01644105):0.19235019):0.09144616,43:0.07884334); END; begin sets; charset exclude = 334 - 396; charset codonPos1 = 1 - 394 \ 3; charset codonPos2 = 2 - 395 \ 3; charset codonPos3 = 3 - 396 \ 3; end; begin mrbayes; set autoclose = no nowarn = yes; exclude 334 - 396; charset codonPos1 = 1 - 394 \ 3; charset codonPos2 = 2 - 395 \ 3; charset codonPos3 = 3 - 396 \ 3; partition currentPartition = 3 : codonPos1 , codonPos2 , codonPos3; set partition = currentPartition; lset applyto = ( 1 , 2 , 3 ); lset nst = 6 rates = invgamma; unlink statefreq = ( all ) revmat = ( all ) shape = ( all ) pinvar = ( all ); prset applyto = ( all ) ratepr = variable; mcmcp ngen = 10000000 relburnin = yes burninfrac = 0.25 printfreq = 1000 samplefreq = 1000 nchains = 4 savebrlens = yes; mcmc; sumt; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 396; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 396; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 396; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1430009334838; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8909467559785029912; tell It; setDefaultOrder 69 41 20 40 43 55 33 34 6 58 25 68 11 37 10 23 39 65 44 19 51 74 63 71 22 31 30 28 62 66 52 46 42 50 14 48 29 60 64 5 27 7 54 21 56 72 12 59 67 75 36 2 32 24 3 18 4 73 13 49 47 17 61 0 16 57 45 70 53 15 38 26 1 9 8 35; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4415335030247869421; checksumv 0 2 568570328 null getNumChars 396 numChars 396 getNumTaxa 76 numTaxa 76 short true bits 15 states 15 sumSquaresStatesOnly 408367.0 sumSquares 408367.0 NumFiles 1 NumMatrices 1; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 716; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8909467559785029912 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1349.1430009254998.9010083041133877328; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 649; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; 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; setTree '((19:0.1492197,(32:0.13310301,((8:0.35775356,7:0.08022409):0.15400399,(4:0.2220578,(76:0.36669064,51:0.25756307):0.18627197):0.15228857):0.26071443):0.11157083):0.26370067,(((((71:0.05748769,63:0.02066869):0.34382027,(17:0.19631156,67:0.01031687):0.06289808):0.09213355,48:0.23454681):0.22263712,6:0.26013414):0.07180057,(49:0.10238167,(31:0.12996546,(68:0.17207037,(((39:0.00514315,38:0.00905971):0.04243126,18:0.0471382):0.11419621,(((41:0.00759715,42:0.00471458):0.20427501,((((27:0.0573605,(((29:0.05195428,(((((((36:0.01035353,(25:1.0E-8,((24:1.0E-8,22:1.0E-8):0.00431733,(23:1.0E-8,21:0.00439289):0.00453946):0.00897759):0.00782359):0.00897954,(75:1.0E-8,74:0.01755727):0.00716851):0.00327618,(28:0.0036131,47:0.01355484):0.00343652):1.0E-8,(30:0.02843345,(13:0.0042745,12:0.00945442):0.00417638):0.00851347):0.00328644,(37:0.01405871,(69:0.03564693,15:0.02068875):1.0E-8):1.0E-8):0.00335622,62:0.01343541):1.0E-8,((45:0.04758002,(26:0.03036711,((53:0.06921182,((((60:1.0E-8,61:1.0E-8):0.00794862,59:0.00340812):0.00518176,58:0.00459213):0.00496482,52:0.00996423):0.00602565):0.00489365,57:0.01017357):0.01046747):0.07437495):0.02672077,16:0.06650714):0.01926076):0.00434004):0.00720879,40:0.04480263):1.0E-8,(10:0.04985621,11:0.01301967):0.13078512):0.05318779):0.01113224,64:0.02766497):0.03976519,(((14:0.3494952,55:0.04286984):0.10660019,(65:0.04449045,66:0.10370997):0.02200823):0.04964666,(((2:0.06263977,9:0.01978062):0.0078903,((50:0.01118829,(73:0.03733843,72:0.00967037):0.20550602):0.00847565,(46:0.04090038,35:0.01764351):1.0E-8):0.00552228):0.0048493,(1:0.05213284,(44:1.0E-8,(33:1.0E-8,34:0.09042275):0.60330559):0.01377035):0.00961479):0.02221192):0.05051476):0.0325065,(54:0.12127171,(70:0.05223865,((56:0.03556718,20:0.01162708):0.03999556,3:0.08674801):0.00386448):0.07469089):0.0371998):0.04020585):0.15857305,(5:0.18379484,43:0.07884334):0.09144616):0.19235019):0.01644105):0.04353027):0.07509554):0.13783043):0.26370067);'; 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; setDigits 4; writeAsPercentage off; 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 #4415335030247869421 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 649; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.SortTaxa.SortTaxa.taxaSort; endTell; setTool mesquite.charMatrices.SortTaxa.SortTaxa.taxaSort; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; 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.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.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;