#NEXUS [written Tue Aug 21 10:31:22 CEST 2012 by Mesquite version 2.75 (build 566) at 1x-193-157-241-103.uio.no/193.157.241.103] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=74; TAXLABELS Adenoides_eludens Akashiwo_sanguinea Alexandrium_affine Alexandrium_fundyense Alexandrium_minutum Amoebophrya_sp_ex_Akashiwo_sanguineaum Amoebophrya_sp_ex_Gymnodinium_instriatum Amphidinium_carterae Amphidinium_massartii Azadinium_obesum Azadinium_spinosum Brachidinium_capitatum Ceratium_furca Ceratium_longipes Ceratocorys_horrida Crypthecodinium_cohnii Cryptosporidium_parvum Dinophysis_acuminata Dinophysis_caudata Duboscquodinium_collinii Eimeria_tenella Ensiculifera_aff_loeblichii Gambierdiscus_australes Gonyaulax_spinifera Gymnodinium_aureolum Gymnodinium_beii Gymnodinium_catenatum Gyrodiniellum_shiwhaense Gyrodinium_dominans Hematodinium_perezi Heterocapsa_pygmaea Heterocapsa_triquetra Karenia_brevis Karenia_mikimotoi Karlodinium_veneficum Kryptoperidinium_foliaceum Lepidodinium_chlorophorum Lepidodinium_viride Lingulodinium_polyedrum Luciella_masanensis Noctiluca_scintillans Ornithocercus_magnificus Ornithocercus_quadratus Oxyrrhis_marina Pentapharsodinium_dalei Pentapharsodinium_tyrrhenicum Peridiniopsis_niei Peridiniopsis_penardii Peridinium_cinctum Peridinium_willei Perkinsus_marinus Pfiesteria_piscicida Phalacroma_cf_rotundatum Phalacroma_rapa Polarella_glacialis Prorocentrum_donghaiense Prorocentrum_lima Prorocentrum_micans Prorocentrum_minimum Protoceratium_reticulatum Protodinium_simplex Pseudopfiesteria_shumwayae Pyrodinium_bahamense Scrippsiella_sweeneyae Scrippsiella_trochoidea Stoeckeria_algicida Symbiodinium_microadriaticum Symbiodinium_sp_C3 Takayama_cf_pulchellum Thecadinium_kofoidii Thoracosphaera_heimii Tintinnophagus_acutus Toxoplasma_gondii Woloszynskia_halophila ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=186; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Adenoides_eludens ACAACTTTCAGTGACGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGCAGA-ATTCCGTGAACCAATAGGGACTTGAACGTATACTGCACT------------TTTGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCGGTG-TCTATTC Akashiwo_sanguinea ACAACTTTCAGCAATGGATACCTCGGCTCGGACACCGATGAA-GGGCGCAG-CGAACTGT-GATAA-GCATTGT-GAATTGCAGA-ATTCCGTGAACCAACAGAATCTTGAACGTATACTGTGCT------------CTCGGGATAT-G--CCT--GAGAGCATGC-CTGCTTCAGTG-TCTCTT- Alexandrium_affine aatatgttttgcaaagaatgtcttagctcaatagatgatgaa-gaatgcag-caaaatgc-aatat-gcattgt-gaattgcaga-attccgtgagccaattgatgtttgaatgttacttgcacc------------ttcgggatat-g--ctt--gaaggtttgc-ttgattcaatg-ccaata- Alexandrium_fundyense attatgttttgcaaagaatgttttagttcaataaatgatgaa-gaatgcag-caaaatgc-attat-gcattgt-gaattgcaga-attccgtgagctaacagatgtttgaatgttacttgtgcc------------tttgggatat-t--ctt--gaaggtttgc-ttgattcaatg-ccaatta Alexandrium_minutum ATGTGTTTTTGCAATGAATGTCTTAGCTCAATTGATGATGAA-GAATGCAG-CAAAATGT-GATAT-GCATTGT-GAATTGCAGA-ATTCCGTGAGCCAATAGATGTTTGAACGTAATTTGCACC------------TTCGGGATAT-G--CTT--GAAGGTGTGC-TTGATTCAATG-TCAATT- Amoebophrya_sp_ex_Akashiwo_sanguineaum -CAACTTTTAGCGATGGATGTCTCGGCTCGAACAACGATGAA-GGACGCCG-CAAAATGC-GATAA-GCGTTGT-GAATGGCAGA-ATTCCGCGAATCAAAAGAAAGCTGAACGCATACTGCACT------------TTCGGGATCC-C--CCT--GAGAGTATGC-TTGGTTCAGGA-CGTTT-- Amoebophrya_sp_ex_Gymnodinium_instriatum ACAACTTTTAGCGGTGGATGTCTCGGCTCAGGCAACGATGAA-GGACGCCG-CAAAATGC-GATAA-GCTTTGT-GAATGGCAGA-ATTCCGCGAATCAATAGAATGCTGAACGCATACTGCACT------------TTTAGGTTAC-T--CCT--GAAAGTATGT-CTAAGTCAGGG-CGTT--- Amphidinium_carterae ataacttccagcagtggatctctaggctcaagtgctgaggaa-gggWgcag-caaagtgt-gataa-gcattgt-gatgtgcgag-atcctgtgaaccattagactcccgatcgcactctgtact------------tctaggat-c-t--cct--ggaagtaatc-cagcttcaggg-tcatgta Amphidinium_massartii -taacttccagcagtggatctcttggctcaagtgctgaggaa-gggtgcag-caaagtgt-gataa-gcattgt-gatgtgcgag-atcctgtgaaccattagactcccgagcgcactctgcact------------ttcaggat-c-c--cct--gaaagtaatc-cagctccaggg-tcatgg- Azadinium_obesum ACAACTTTCAGCGACGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-ACATTGT-GAATTGCAGA-ATTCCGTGAACCAATAGGGATTTGAACGTATACTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTG-CCTCTAC Azadinium_spinosum ACAACTTTCAGCGACGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-ACATTGT-GAATTGCAGA-ATTCCGTGAACCAATAGGGATTTGAACGTATACTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTG-CCTCTAC Brachidinium_capitatum ACAACTTTCAGCGACGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGCAGA-ATTCCGTGAACCAATAGGGATTTGAACGTATACTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTG-TCAAGAT Ceratium_furca acaaatttcagcaacagatgtcttggttcacatgttgatgaa-gggtgcag-cgaagtgc-aataa-tcattgt-gaattgcaga-attccgtgaatcaattgaccattgaacgcaga-agtgcc------------cttggggcat-t--cct--gagggcatgc-ttgtgtcagtg-tttaata Ceratium_longipes ----atttcagcaacagatgtcttggttcacatgttgatgaa-gggtgcag-cgaagtgc-agtaa-tcattgt-gaattgcaga-attccgtgaatcaattgaccattgaacgcaga-agtgcc------------cttggggcat-t--cct--gagggcatgc-ttgtgtcagtg-ttttc-- Ceratocorys_horrida aacaccttcagtgatggatgctttggttcaaacaatgatgaa-gggtgcag-tgaaatgt-attag-gcattgt-gaattgcaga-attccgtgaaccaatggtgcattgaacatatactatgtt------------ttcaggatat-t--cct--gcaagcatgc-ttgaatcagtg-ccatg-- Crypthecodinium_cohnii ACAACTTTCAGCAGTTGATTCCTTGGTTCAGACCTCGATGAA-GGGCACTG-CGAAATGT-GAATG-GCATTGT-GAATTGCAGG-CATCCGGGAATTGAGAGCTTCTTGAATGCATACTGCTCCAGCTGACTTGTCAGTTGGATAATCTTCCTCAGGGACTATGTACTCCCTCGATG-CTTCATC Cryptosporidium_parvum -acactttaagtaatggatgtcttggttctcataacgatgaa-ggacgcag-caaagtgc-gataa-gcaatgt-gaactgcata-attctatgaacaatcagatctctcaacgcaaatagca-------------------gtaat-t--tac--attactatat-ttatatcagtg-tctatta Dinophysis_acuminata acaattttcagcgatggatgcctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-tctttgt-gaattgcaga-attccgtgaatcaatagagctttgaacgtgtcttgcgct------------ttcgggctat-a--cct--gaaagcatgc-ctgcgttggtg-------- Dinophysis_caudata -CAATTTTCAGCGATGGATGCCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-TCTTTGT-GAATTGCAGA-ATTCCGTGAATCAATAGAGCTTTGAACGTGTTTTGCGCT------------TTCGGGCTAT-A--CCT--GAAAGCATGC-CTGCGTTGGTG-TCTG--- Duboscquodinium_collinii ACAACTTTCAGCGATCGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGCAGG-ATTCCGTGAACCAATGGGGACTTGAACGTACACTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTGTCCACTTC Eimeria_tenella -aaactttcagcaatggatgtcttggctcacgcatcgatgaa-ggacgcag-cgaaatgc-gatac-gcattgt-gaattgcaga-tttcagtgaaccatcagatttctgaacgcacatggcgct------------gctggtattt-t--gcc--cgcagcacgt-ctgtttcagtg-tctct-- Ensiculifera_aff_loeblichii ACAACTTTCAGCGATGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCAWTGT-GAATTGCAGA-ATTCCGTGAACCAATAGGGACTTGAACGTACACTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTACTTCAGTG-TCTA--- Gambierdiscus_australes AACTTTCAACG-AATGAATGTCTCGGCTCGAGCAACGATGAACGGGCGCAGTCGAAGTGTTGATTGAGCAATGT-GAATTGCAGATTTCCCGTGAACCAATAGGGATTTGAACGTATGCTGTACT------------TTTGGAATAG-C--CCT--GAGAGTATGC-CTCCTTCAGTTGTCAAATG Gonyaulax_spinifera acttttttcaggtgtggatgccttagctcaaacgttgatgaa-gggtgtag-tgaaatgc-gaaat-gcaatgt-gacatgcaaa-accccgtgaaccaattggttgttgaatgttgcctttgct------------ttcaagtact-t--cct--ggaagcatgt-cctcttcattg-atgt--- Gymnodinium_aureolum acaactttcagcgatggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgc-gataa-gcattgt-gaattgcaga-attccgtgaaccgacaggaacttgaacgcatattgtgct------------tttgggatat-c--cct--gaaagcatgc-ctgcttcagtg-t------ Gymnodinium_beii ACAACTTTCAGCGACGGATATCTCGGCTCAAGCACCGATGAA-GGGCGCAG-CGAAGTGT-GATAA-TCATTGT-GAATTGCAGA-ATTCCGTGAACCAATGGATCTTTGAACGTGCATTGCACT------------CTGGGGATAT-C--CCT--GGGAGTATGC-CTGCTTCAGTG-CTTGTGG Gymnodinium_catenatum acaactttcagcgacggatgtctcggttcgaacaacgatgaa-gggcgcag-cgaagtgc-gataa-gcattgt-gaattgcaga-attccgtgaaccgacagaaacttgaacgcatattgtgct------------tttgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tctatgt Gyrodiniellum_shiwhaense ACAACTTTCAGCGATGGATATCTCGGTTCGATCAACGATGAA-GGGCGCAG-CGAAGTGC-GATAA-GCATTGT-GAATTGCAGA-ATTCCGTGAACCGACAGGGACTTGAACGCATATTGTGCT------------TTTGGGATAT-C--CCC--GAAAGCATGC-CTGCTTCAGTG-TCTATGC Gyrodinium_dominans ACAACTTTCAGCGACGGATGTCTCGGCTCAAACAACGATGAA-GGGCGCAG-CGAAGTGC-GATAA-GCATTGC-GACTTGCAGA-ATTCCGTGAACCAACAGATTCCTGAACGTATACTGCGCT------------TTCGGGATAC-C--CCT--GAAAGCATGC-CTACTTCAGTGTCATC--- Hematodinium_perezi ------------------------------GGTTACGATGAA-GGACGCAG-CGAATTGC-GATAA-GCAATGC-GAATTGCAGA-ATTCCGTGAATCATCAGATTTTTGAACGTACTCTACGCT------------CTCGGG-TAT-C--CCT--GGGAGCATGTCTGGTCTCAGCGTCTGTTCA Heterocapsa_pygmaea acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggatttgaacgtacactgcgct------------ttcgggacat-c--cct--gaaagcatgc-ttgcttcagtg-tctactc Heterocapsa_triquetra -------tcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggatttgaacgtacactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tctactc Karenia_brevis acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggatttgaacgtatactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tc----- Karenia_mikimotoi acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggatttgaacgtatactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tcaatat Karlodinium_veneficum acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggatttgaacgtatactgcgct------------ttcgggttat-t--cct--gaaagcatgc-cttcttcagtg-tctac-- Kryptoperidinium_foliaceum AACACTTTCAGCGATGGATACCTTGGCTCGAACAACAATGAA-GGGTGCAG-CGAAGTGC-GAGAA-GCATTGT-GAATTGCAGA-ATTCCGTGAGCCAATTGAAAACTGAATGTATATTGCGCT------------TTCGGGAAAT-G--CCT--GAGAGCATGC-CTACTTCAGCG-TCCATT- Lepidodinium_chlorophorum ACAACTTTCAGCGATGGATGTCTCGGTTCGATCAACGATGAA-GGGCGCAG-CGAAGTGC-GATAA-GCATTGT-GAATTGCAGA-TTTCCGTGAACCGACAGGGACTTGAACGCATATTGTGCT------------TTTGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTG-TCTACGC Lepidodinium_viride acaactttcagcgatggatgtctcggttcgatcaacgatgaa-gggcgcag-cgaagtgc-gataa-gcattgt-gaattgcaga-tttccgtgaaccgacagggacttgaacgcatattgtgct------------tttgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tctacg- Lingulodinium_polyedrum gtgttattcagtaatggatgccttggtctgaaaatcgatgaa-gagtacag-cgaaatgt-gatat-gcattgt-gaactgcaga-cttccgtgagtcaatggcttgttgaacgtttgctgtgcc------------tttgggatac-g--cct--gaaggcgcgc-ctgcttcagcg-tctgttc Luciella_masanensis ACAACTTTCAGCGACGAATGTCTCGGCTCGAACAACGATGAA-GGGCACAG-CGAACTGT-GATAA-GCATTGT-GAATTGCAGA-TTTCCGCGAATCAATAGAAACTTGAACGTAAAATGCGGT------------TTCGGGATAT-C--CCT--GAAACCATGC-CTGCTTCAGTGTCCCAACC Noctiluca_scintillans ataacttccagtgatggatgtctcggctcgaacaacgatgaa-gggtgcag-cgaagtgt-gataa-gcattgt-gaattgcagg-attcagtgaaccaacagaaagttgaacgcatattgctct------------ttcgggttat-t--cct--gaaagcatgt-ttacttcagtg-tctttt- Ornithocercus_magnificus -CAACTTTCAGCGATGGATGTCTCGGCTCGGACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-CCTTTGT-GAATTGCAGA-ATTCCGTGAATCAATAGAGCTTTGAACGTGTTTTGTGCT------------TTTGGGATAT-A--CCT--GAAAGCATGC-CTGCTTTGGTG-TCTA--- Ornithocercus_quadratus -CAACTTTCACCGATGGAGGTCTCGGCTCGGACAACAATAAA-AGGGGCAC-CGAAATGT-GATAA-CCTTTGT-GAATTGCAAA-AATCCCTGAATCAATAAAGCTTTTAACGTGTTTTGTGCT------------TTTGGGATAT-A--CCC--GAAAGCATGC-CCGCTTTGGGG-TCTA--- Oxyrrhis_marina GAAAAGCGCAGCGACGAATTTCTAGAATCAATAATCGAAGAC-GAGCGCAG-CAAATTGC-GAAAA-GCAAAAC-GATATGCTGA-TGATCGAGATGTTCAGGCAATTCTAATACAGGAAGTGGGACAG--------TTGTGTCTCGTCTTTGTTGCAGGGTAT-C---GGAACATGT--GTTTAT Pentapharsodinium_dalei ACAACTTTCAGCGACGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGcaca-atTCCGTGAACCAATAGGGACTTGAACGTACACTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTG-TCTATTC Pentapharsodinium_tyrrhenicum acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggacttgaacgtacactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tctattc Peridiniopsis_niei ACAACTTTCAGCGACGGATATCTCGGCTCAAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGCAGA-TTTCCGTGAGCCAATAGAAACCTGAACGCATCCTGCGCT------------TTCGGGATAT-T--CCT--GAAAGCATGC-CTGCTTCAGTG-TCTACTT Peridiniopsis_penardii ACAACTTTCAGCGACGGATATCTCGGCTCAAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGCAGA-TTTCCGTGAGCCAATAGAAACCTGAACGCATCCTGCGCT------------TTCGGGATAT-T--CCT--GAAAGCATGC-CTGCTTCAGTG-TCTACTT Peridinium_cinctum accacattcagtgacggatgtcttggctcgagcagcgatgaa-gggcgcag-cgaactgc-gatac-gcattgt-gaattgcaga-attctgtgaatcaatagagacttgaatgcgcactgcgtt------------tttgggacat-c--cct--aaaagcaggc-ctgcttcagtg-tccgtgc Peridinium_willei accacattcagcaatggatgtcttggcttgagcaatgatgaa-gggcgcag-cgaactgc-gatac-gcactgt-gaattgcaaa-attccgtgagtcaatagagacttgaacgtgcagtgtgct------------tctgggatat-t--cct--gaaagtatgc-ctgcttcagtg-tctgtt- Perkinsus_marinus --aactctcaacgatggatgcctcggctcgagaatcgatgaa-ggacgcag-cgaagtgc-gataa-gcactgc-gatttgcaga-attccgtgaaccagtagaaatctcaacgcatactgcaca------------aaggggatct-tt-cct--ctttgtacat-acatatcagtg-tcgctc- Pfiesteria_piscicida acaactttcagcgatcgatgtctcggctcgaacaacgatgaa-gggcacag-cgaactgt-gataa-gcattgt-gaattgcaga-attccgtgaatcaatagaaacttgaacgtaaaatgcggt------------ttcgggatat-c--cct--gaaaccatgc-ctgcttcagtg-tccca-- Phalacroma_cf_rotundatum -CAACCTTCAGCGATGGATGTCTCGGCTTGGACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-CCTTTGT-GAATTGCAGA-ATTCCGTGAATCAATAGAGCTTTGAACGCGTGTTGTGCT------------GTTGGGATAT-A--CCT--GACAGCATGC-CTGCTTTGGTG-CCTT--- Phalacroma_rapa ----------------------tcggcttggacaacattgaa-gggcgcag-cgaagtgt-gataa-cctttgt-gaattgcaga-attccgtgaatcaatagagcattgaacgcgtgctgtgct------------gttgggatat-a--cct--gacagcatgc-ctggtttggcg-tcttctg Polarella_glacialis acaactttcagcgacggatatctcggctcaagcatcgatgaa-gggcgcag-cgaagtgt-gataa-tcattgt-gaattgcaga-attccgtgaaccaatggaaacttgaacgtgcattacact------------ctcgggatat-c--cct--gggagtatgc-ctgcttcagtg-cttgtgg Prorocentrum_donghaiense acaactttcagcgacggatgtctcggctcgaacaacaatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggacttgaacgtatactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tcta--- Prorocentrum_lima ACAACTTTCAGCGACGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGCAGA-ATTCCGTGAACCAATAGGGACTTGAACGTATACTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTG-TCTATTC Prorocentrum_micans acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggacttgaacgtatactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tctattc Prorocentrum_minimum acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggacttgaacgtatactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tctattc Protoceratium_reticulatum ---agcttcagtgatggatgctttggttcaaacaacgatgaa-gggtgcag-tgaaatgt-attag-gcattgt-gaattgcaga-attccgtgaaccaatggggcattgaacgtattctatgtt------------tttgggacat-t--cct--gcaagcatgc-ttgaatcagtg-ccatgtc Protodinium_simplex acaactttcagcgacggatatctcggctcaagcatcgatgaa-gggcgcag-cgaagtgt-gataa-tcattgt-gaattgcaga-attccgtgaaccaatggattcttgaacgtgcattgcact------------ctcgggatat-c--cct--gggagtatac-ctgcttcagtg-cttgtgg Pseudopfiesteria_shumwayae acaactttcagcgatcgatgtctcggctcgaacaacgatgaa-gggcacag-cgaactgt-gataa-gcattgt-gaattgcaga-attccgtgaatcaatagaaacttgaacgtaaaatgcggt------------ttcgggatat-c--cct--gaaaccatgc-ctgcttcagtg-tccca-- Pyrodinium_bahamense acaaggttcagcgatggatgtttcggcttagttgatgataaa-gggcgcag-caaaatgt-gatac-gcattgt-gaattgcagg-attccgtgaactaattggtttttgaatgcacgttgcacc------------tttgggatat-t--cct--caaggtgtgc-ttgattcaatg-tcttgc- Scrippsiella_sweeneyae acaactttcagcgatcgatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcagg-attccgtgaaccaatagggacttgaacgtacactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tccactt Scrippsiella_trochoidea acaactttcagcgacggatgtctcggctcgaacaacgatgaa-gggcgcag-cgaagtgt-gataa-gcattgt-gaattgcaga-attccgtgaaccaatagggacttgaacgtacactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tctattc Stoeckeria_algicida acaactttcagcgattgatgtctcggctcgaacaacgatgaa-gggcacag-cgaactgt-gataa-gcattgt-gaattgcaga-attccgtgaatcaatagaaacttgaatgtagactgtgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tccaa-- Symbiodinium_microadriaticum acaattttcagcgacggatatcttggctcgagcacctatgaa-gggcgcag-cgaagtgc-gataa-tcgttgt-gaattgcaga-actccgtgaaccaatggcctcttgaacgtgcattgcgct------------cttgggatat-g--cct--gagagcatgt-ctgcttcagtg-cttctac Symbiodinium_sp_C3 acaactttcagcgatggatatcttggctcgggcacctgtgaa-gggcgcag-cgaagcgc-gatag-tctttgt-gaattgcaga-actccatgaaccaatggcctcctgaatgtgcgttgcact------------cttgggat-t-t--cct--gagagtatgt-ctgcttcagtg-cttaact Takayama_cf_pulchellum ACAACTTTCAGCGACGGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAGTGT-GATAA-GCATTGT-GAATTGCAGA-ATTCCGTGAACCAATAGGGATTTGAACGTATACTGCGCT------------TTCGGGACAT-T--CCT--GAAAGCATGC-CTGCTTCAGTG-TCTACTG Thecadinium_kofoidii ACAGCTTTCAGTGATGGATGACTTGGCTCAAACAAAGATGAA-GGGTGCAG-CGAAATGC-GATAA-GCATTGT-GAATTGCAGA-ATTCCGTGAACCAATGGGGTTTTGAACGTATACTGCGCT------------TTTGGGATGT-C--CCT--GAAAGCATGC-CTCCTTCAGGG-TCTTCTG Thoracosphaera_heimii -caactttcagcgatcgatgtctcggctcgaacaacgatgaa-gggcgcag-cgaactgt-gataa-gcattgt-gaattgcaga-attccgagaaccaatagaaccttgaacgcaaactgcgct------------ttcgggatat-c--cct--gaaagcatgc-ctgcttcagtg-tcc---- Tintinnophagus_acutus -CCATCTTCAGCGATTGATGTCTCGGCTCGAACAACGATGAA-GGGCGCAG-CGAAATGC-GATAC-GCATTGT-GACTTGCAGA-ATTCCGTGAACCAACAGAAACTTGAACGTATATTGCGCT------------TTCGGGATAT-C--CCT--GAAAGCATGC-CTGCTTCAGTG---TCCAT Toxoplasma_gondii -aaattttcagcaatggatgtcttggctcgcgcaacgatgaa-ggacgcag-cgaactgc-gaaac-gcaatgtggaattgcaga-attcagtgaatcatcagatttctgaacgca----atgca------------cctgggatat-c--tcc--tg--gtacgt-ctgtttcagtg-tcttt-- Woloszynskia_halophila acaactttcagcgacggatatctcggctcaagcaccgatgaa-gggcgcag-cgaagtgt-gataa-tcattgt-gaattgcaga-attccgtgaaccaatggattcttgaacgtgcattgcact------------ctcgggatat-c--cct--gggagtatgc-ctgcttcagtg-cttgtgg ; END; BEGIN MacClade; Version 4.0 86; LastModified -866661414; FileSettings editor '0' '0' '1' '1'; Singles 000; Editor 00011001111111100100010010 '1' '12' Geneva '9' '344' '1' all; EditorPosition '46' '6' '771' '1039'; TreeWindowPosition '46' '6' '799' '1102'; ListWindow Characters closed Geneva '9' '50' '10' '129' '399' 000; ListWindow Taxa closed Geneva '9' '50' '10' '129' '490' 1000000; ListWindow Trees closed Geneva '9' '50' '10' '276' '490'; ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ListWindow ExSets closed 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END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 186; EXSET * UNTITLED = 1 - 3 43 52 61 67 75 86 126 - 137 148 150 - 151 155 - 156 167 179 - 186; END; BEGIN CODONS; CODONPOSSET * UNTITLED = N: 1- 186 ; CODONPOSSET CodonPositions = N: 1- 186 ; CODESET * UNTITLED = universal: 1 - 186; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 186; END; BEGIN TREES; Title 'Trees from "S5_58s.tree"'; LINK Taxa = Taxa; TRANSLATE 1 Adenoides_eludens, 2 Akashiwo_sanguinea, 3 Alexandrium_affine, 4 Alexandrium_fundyense, 5 Alexandrium_minutum, 6 Amoebophrya_sp_ex_Akashiwo_sanguineaum, 7 Amoebophrya_sp_ex_Gymnodinium_instriatum, 8 Amphidinium_carterae, 9 Amphidinium_massartii, 10 Azadinium_obesum, 11 Azadinium_spinosum, 12 Brachidinium_capitatum, 13 Ceratium_furca, 14 Ceratium_longipes, 15 Ceratocorys_horrida, 16 Crypthecodinium_cohnii, 17 Cryptosporidium_parvum, 18 Dinophysis_acuminata, 19 Dinophysis_caudata, 20 Duboscquodinium_collinii, 21 Eimeria_tenella, 22 Ensiculifera_aff_loeblichii, 23 Gambierdiscus_australes, 24 Gonyaulax_spinifera, 25 Gymnodinium_aureolum, 26 Gymnodinium_beii, 27 Gymnodinium_catenatum, 28 Gyrodiniellum_shiwhaense, 29 Gyrodinium_dominans, 30 Hematodinium_perezi, 31 Heterocapsa_pygmaea, 32 Heterocapsa_triquetra, 33 Karenia_brevis, 34 Karenia_mikimotoi, 35 Karlodinium_veneficum, 36 Kryptoperidinium_foliaceum, 37 Lepidodinium_chlorophorum, 38 Lepidodinium_viride, 39 Lingulodinium_polyedrum, 40 Luciella_masanensis, 41 Noctiluca_scintillans, 42 Ornithocercus_magnificus, 43 Ornithocercus_quadratus, 44 Oxyrrhis_marina, 45 Pentapharsodinium_dalei, 46 Pentapharsodinium_tyrrhenicum, 47 Peridiniopsis_niei, 48 Peridiniopsis_penardii, 49 Peridinium_cinctum, 50 Peridinium_willei, 51 Perkinsus_marinus, 52 Pfiesteria_piscicida, 53 Phalacroma_cf_rotundatum, 54 Phalacroma_rapa, 55 Polarella_glacialis, 56 Prorocentrum_donghaiense, 57 Prorocentrum_lima, 58 Prorocentrum_micans, 59 Prorocentrum_minimum, 60 Protoceratium_reticulatum, 61 Protodinium_simplex, 62 Pseudopfiesteria_shumwayae, 63 Pyrodinium_bahamense, 64 Scrippsiella_sweeneyae, 65 Scrippsiella_trochoidea, 66 Stoeckeria_algicida, 67 Symbiodinium_microadriaticum, 68 Symbiodinium_sp_C3, 69 Takayama_cf_pulchellum, 70 Thecadinium_kofoidii, 71 Thoracosphaera_heimii, 72 Tintinnophagus_acutus, 73 Toxoplasma_gondii, 74 Woloszynskia_halophila; TREE tree_1 = (((((((((((((((((((((((((((3:0.0019004846863590608,4:0.08736564500766608):0.08589743017364837,5:0.012507884434151961):0.15908277219929978,63:0.14933517666570228):0.1065562436555938,(13:1.8588456942580933E-6,14:0.007609481519203154):0.2659938041862482):0.06574896798907748,39:0.30427055334748765):0.05973817892917088,(60:0.025789467513634534,15:0.03936602069293471):0.1764205042138034):1.8588456942580933E-6,70:0.07084351518078913):0.06574722069979444,((23:0.24931195422178476,35:0.008546090298837239):0.00737645112041152,69:0.008014068757851156):0.007088071779768335):1.8588456942580933E-6,(((12:1.8588456942580933E-6,33:1.8588456942580933E-6):1.8588456942580933E-6,34:1.8588456942580933E-6):1.8588456942580933E-6,(11:1.8588456942580933E-6,10:1.8588456942580933E-6):0.00750912238422341):1.8588456942580933E-6):0.007498331481013754,1:0.03045963946168806):1.8588456942580933E-6,((56:0.007506620344190029,57:1.8588456942580933E-6):1.8588456942580933E-6,58:1.8588456942580933E-6):1.8588456942580933E-6):1.8588456942580933E-6,59:1.8588456942580933E-6):0.007166994390997772,45:0.007561292873550229):1.8588456942580933E-6,(65:1.8588456942580933E-6,46:1.8588456942580933E-6):1.8588456942580933E-6):1.8588456942580933E-6,(31:0.015138954062797527,32:1.8588456942580933E-6):0.007515410645630105):0.0072966241236973595,22:0.007764748435167501):1.8588456942580933E-6,(20:0.0074638897775667346,64:1.8588456942580933E-6):0.01532686709252129):0.011470769345224952,(((((53:1.8588456942580933E-6,54:0.05589088607480974):0.04872839183008493,42:1.8588456942580933E-6):1.8588456938140041E-6,43:0.14163844311982787):0.022261995351464225,(18:0.007368576004788352,19:1.8588456942580933E-6):0.041576899163428216):0.09107504324940852,(49:0.08921179270732393,50:0.10403125740922059):0.07282647703985967):0.016689727626723716):0.011890420379914612,((((((55:0.023097854243923077,61:0.007706324765658135):0.0068888862815921215,74:1.8588456942580933E-6):1.8588456938140041E-6,26:0.022710449138505062):0.02686501278660547,(68:0.10159099326849796,67:0.018129354593968472):0.08531277894223699):0.0743489898327212,2:0.06212599574644351):0.03439707203998399,((48:1.8588456942580933E-6,47:1.8588456942580933E-6):0.04357520204304155,36:0.14088508012749745):0.018808342664671684):0.011017274498300367):1.8588456942580933E-6,(((((62:1.8588456942580933E-6,52:1.8588456942580933E-6):1.8588456942580933E-6,40:0.039261226004415395):0.015786749278320134,16:0.5856582900209109):0.009324372319259311,66:0.029751963688905203):0.015449646914139414,71:0.0240618277844189):0.02417870504180497):0.017232279755175828,((((8:0.05066782255494218,9:0.011340903987959727):0.3508874321268971,24:0.4966525640404522):0.0886968875878491,29:0.015322765801321747):0.04891081358745941,72:0.04735757865838108):0.008859769192288258):0.008824601998751458,((((37:1.8588456942580933E-6,38:1.8588456942580933E-6):0.007485256635616722,28:0.015239611631205907):0.023105976345262125,27:0.02068140035813748):0.0073454053430732635,25:1.8588456942580933E-6):0.03679609114692939):0.0059499762673751455,41:0.11446939999328132):0.03324266798058639,51:0.35494516081187877):1.8588456938140041E-6,(7:0.11669853246303052,6:0.058776231533198775):0.14301547062605113):0.09945783789821627,30:0.18091441972134126):0.04691495978520439,(((44:2.4720518182186186,73:1.8588456942580933E-6):0.06517449428119404,21:0.11237398647818919):0.053718506350032946,17:0.3655708781550757):0.04691495978520426); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1345537883020; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1969999848099233909; tell It; setDefaultOrder 40 71 66 4 3 59 60 44 43 37 38 47 1 0 2 39 62 10 11 27 63 69 65 6 46 21 45 68 73 67 22 23 48 49 50 24 52 51 8 70 58 14 15 72 31 32 41 42 25 26 61 33 13 12 16 54 55 56 57 5 20 34 7 28 29 36 17 18 53 9 35 30 64 19; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4846135411224074184; mqVersion 275; checksumv 0 3 1540067969 null getNumChars 186 numChars 186 getNumTaxa 74 numTaxa 74 short true bits 3458764513820540943 states 15 sumSquaresStatesOnly 260758.0 sumSquares -5.397978484569258E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 135; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1023 661; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #1969999848099233909 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #1969999848099233909; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 888 594; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.sort; 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.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4846135411224074184 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 213; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 888 594; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; togglePaleInapplicable on; toggleShowBoldCellText 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.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; 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.chromaseq.ColorQuality.ColorQuality; tell It; toggleAmbiguities on; toggleMarks on; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; getEmployee #mesquite.chromaseq.SourceFileInfoEditor.SourceFileInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;