# E: Estimate gene trees, orthogroup members, etc. # D: Draw phylogenetic trees. # S: Summarize results. >Mode S >QuerySpecies Ciona-intestinalis # SpaciesName_color Amino acide database Nucleotide database >TaxonSampling Streptomyces-coelicolor_Black 000_OnlyLongestPEP_Streptomyces_coelicolor_a3_2_.ASM20383v1.pep.all.fa 000_OnlyLongestCDS_Streptomyces_coelicolor_a3_2_.ASM20383v1.cds.all.fa Arabidopsis-thaliana_Black 000_OnlyLongestPEP_Arabidopsis_thaliana.TAIR10.pep.all.fa 000_OnlyLongestCDS_Arabidopsis_thaliana.TAIR10.cds.all.fa Saccharomyces-cerevisiae_Black 000_OnlyLongestPEP_Saccharomyces_cerevisiae.R64-1-1.pep.all.fa 000_OnlyLongestCDS_Saccharomyces_cerevisiae.R64-1-1.cds.all.fa Capsaspora-owczarzaki_Black 000_OnlyLongestPEP_GCF_000151315.2_C_owczarzaki_V2_rna.gbff.txt 000_OnlyLongestCDS_GCF_000151315.2_C_owczarzaki_V2_rna.gbff.txt Salpingoeca-rosetta_Black 000_OnlyLongestPEP_S-rosetta_GCF_000188695.1_Proterospongia_sp_ATCC50818_rna.gbff.txt 000_OnlyLongestCDS_S-rosetta_GCF_000188695.1_Proterospongia_sp_ATCC50818_rna.gbff.txt Monosiga-brevicollis_Black 000_OnlyLongestPEP_Monosiga-brevicollis_GCF_000002865.3_V1.0_rna.gbff.txt 000_OnlyLongestCDS_Monosiga-brevicollis_GCF_000002865.3_V1.0_rna.gbff.txt Amphimedon-queenslandica_Black 000_OnlyLongestPEP_Amphimedon_queenslandica.Aqu1.pep.all.fa 000_OnlyLongestCDS_Amphimedon_queenslandica.Aqu1.cds.all.fa Trichoplax-adhaerens_Black 000_OnlyLongestPEP_Trichoplax_adhaerens.ASM15027v1.pep.all.fa 000_OnlyLongestCDS_Trichoplax_adhaerens.ASM15027v1.cds.all.fa Thelohanellus-kitauei_Black 000_OnlyLongestPEP_Thelohanellus_kitauei.ASM82789v1.pep.all.fa 000_OnlyLongestCDS_Thelohanellus_kitauei.ASM82789v1.cds.all.fa Hydra-vulgaris_Black 000_OnlyLongestPEP_Hydra-vulgaris_rna.gbk.txt 000_OnlyLongestCDS_Hydra-vulgaris_rna.gbk.txt Acropora-digitifera_Black 000_OnlyLongestPEP_Acropora-digitifera_rna.gbk.txt 000_OnlyLongestCDS_Acropora-digitifera_rna.gbk.txt Mnemiopsis-leidyi_Black 000_OnlyLongestPEP_Mnemiopsis_leidyi.MneLei_Aug2011.pep.all.fa 000_OnlyLongestCDS_Mnemiopsis_leidyi.MneLei_Aug2011.cds.all.fa Schistosoma-mansoni_Black 000_OnlyLongestPEP_Schistosoma_mansoni.ASM23792v2.pep.all.fa 000_OnlyLongestCDS_Schistosoma_mansoni.ASM23792v2.cds.all.fa Capitella-teleta_Black 000_OnlyLongestPEP_Capitella_teleta.Capitella_teleta_v1.0.pep.all.fa 000_OnlyLongestCDS_Capitella_teleta.Capitella_teleta_v1.0.cds.all.fa Notospermus-geniculatus_Black 000_OnlyLongestPEP_Notospermus-geniculatus_nge_genome_v2.0_prot.fa 000_OnlyLongestCDS_Notospermus-geniculatus_nge_genome_v2.0_nucl.fa Phoronis-australis_Black 000_OnlyLongestPEP_Phoronis-australis_pau_genome_v2.0_prot.fa 000_OnlyLongestCDS_Phoronis-australis_pau_genome_v2.0_nucl.fa Octopus-bimaculoides_Black 000_OnlyLongestPEP_Octopus_bimaculoides.PRJNA270931.pep.all.fa 000_OnlyLongestCDS_Octopus_bimaculoides.PRJNA270931.cds.all.fa Biomphalaria-glabrata_Black 000_OnlyLongestPEP_Biomphalaria-glabrata_rna.gbk.txt 000_OnlyLongestCDS_Biomphalaria-glabrata_rna.gbk.txt Crassostrea-gigas_Black 000_OnlyLongestPEP_Crassostrea_gigas.oyster_v9.pep.all.fa 000_OnlyLongestCDS_Crassostrea_gigas.oyster_v9.cds.all.fa Pinctada-fucata_Black 000_OnlyLongestPEP_Pinctada-fucata_pfu_aug2.0.AA1.fasta 000_OnlyLongestCDS_Pinctada-fucata_pfu_aug2.0.NT1.fasta Priapulus-caudatus_Black 000_OnlyLongestPEP_Priapulus-caudatus_rna.gbk.txt 000_OnlyLongestCDS_Priapulus-caudatus_rna.gbk.txt Trichinella-spiralis_Black 000_OnlyLongestPEP_Trichinella_spiralis.Tspiralis1.pep.all.fa 000_OnlyLongestCDS_Trichinella_spiralis.Tspiralis1.cds.all.fa Caenorhabditis-elegans_Black 000_OnlyLongestPEP_Caenorhabditis_elegans.WBcel235.pep.all.fa 000_OnlyLongestCDS_Caenorhabditis_elegans.WBcel235.cds.all.fa Limulus-polyphemus_Black 000_OnlyLongestPEP_Limulus-polyphemus_rna.gbk.txt 000_OnlyLongestCDS_Limulus-polyphemus_rna.gbk.txt Strigamia-maritima_Black 000_OnlyLongestPEP_Strigamia_maritima.Smar1.pep.all.fa 000_OnlyLongestCDS_Strigamia_maritima.Smar1.cds.all.fa Hyalella-azteca_Black 000_OnlyLongestPEP_Hyalella-azteca_rna.gbk.txt 000_OnlyLongestCDS_Hyalella-azteca_rna.gbk.txt Pediculus-humanus_Black 000_OnlyLongestPEP_Pediculus_humanus.PhumU2.pep.all.fa 000_OnlyLongestCDS_Pediculus_humanus.PhumU2.cds.all.fa Zootermopsis-nevadensis_Black 000_OnlyLongestPEP_Zootermopsis_nevadensis.ZooNev1.0.pep.all.fa 000_OnlyLongestCDS_Zootermopsis_nevadensis.ZooNev1.0.cds.all.fa Rhodnius-prolixus_Black 000_OnlyLongestPEP_Rhodnius_prolixus.RproC3.pep.all.fa 000_OnlyLongestCDS_Rhodnius_prolixus.RproC3.cds.all.fa Nasonia-vitripennis_Black 000_OnlyLongestPEP_Nasonia_vitripennis.Nvit_2.1.pep.all.fa 000_OnlyLongestCDS_Nasonia_vitripennis.Nvit_2.1.cds.all.fa Dendroctonus-ponderosae_Black 000_OnlyLongestPEP_Dendroctonus_ponderosae.DendPond_male_1.0.pep.all.fa 000_OnlyLongestCDS_Dendroctonus_ponderosae.DendPond_male_1.0.cds.all.fa Bombyx-mori_Black 000_OnlyLongestPEP_Bombyx_mori.ASM15162v1.pep.all.fa 000_OnlyLongestCDS_Bombyx_mori.ASM15162v1.cds.all.fa Drosophila-melanogaster_Black 000_OnlyLongestPepsTranslated_Drosophila_melanogaster.BDGP6.cds.pep.all.fa 000_OnlyLongestCDStrans_Drosophila_melanogaster.BDGP6.cds.all.fa Strongylocentrotus-purpuratus_Green 000_OnlyLongestPEP_Strongylocentrotus_purpuratus.Spur_3.1.pep.all.fa 000_OnlyLongestCDS_Strongylocentrotus_purpuratus.Spur_3.1.cds.all.fa Acanthaster-planci_Green 000_OnlyLongestPEP_Acanthaster-planci_oki-cotsv1.0.EVM2a.prot 000_OnlyLongestCDS_Acanthaster-planci_oki-cotsv1.0.EVM2a.mrna Saccoglossus-kowalevskii_Purple 000_Saccoglossus-kowalevskii_sko.prot.txt 000_Saccoglossus-kowalevskii_sko.cds.txt Ptychodera-flava_Purple 000_Ptychodera-flava_pfl.prot.txt 000_Ptychodera-flava_pfl.cds.txt Branchiostoma-belcheri_Orange 000_OnlyLongestPEP_Branchiostoma.belcheri_v18h27.r3_Translated.fa 000_OnlyLongestCDS_Branchiostoma.belcheri_v18h27.r3_ref_cds.fa Branchiostoma-floridae_Orange 000_OnlyLongestPEP_Branchiostoma-floridae_proteins.Brafl1_21954.fasta 000_OnlyLongestCDS_Branchiostoma-floridae_transcripts.Brafl1_21954.fasta Gallus-gallus-E102_Magenta 000_OnlyLongestPEP_Gallus_gallus-E102.GRCg6a.pep.all.fa 000_OnlyLongestCDS_Gallus_gallus-E102.GRCg6a.cds.all.fa Homo-sapiens-E102_Magenta 000_OnlyLongestPEP_Homo_sapiens-E102.GRCh38.pep.all.fa 000_OnlyLongestCDS_Homo_sapiens-E102.GRCh38.cds.all.fa Oikopleura-dioica_Blue 000_OnlyLongestPEP_Oikopleura_peptides_reference_v1.0a.fa.txt 000_OnlyLongestCDS_Oikopleura_transcripts_reference_v1.0.fa.txt Salpa-thompsoni_Blue 005_Salpa-thompsoni_longest_orfs.pep 005_Salpa-thompsoni_longest_orfs.cds Botrylloides-leachii_Blue 005_PEP_Boleac_proteins_v4.fasta 005_CDS_Boleac_transcripts_v5.fasta Botryllus-schlosseri_Blue 000_PEP_Botryllus-schlosseri_start_stop_transcripts30.fa.txt 000_CDS_Botryllus-schlosseri_start_stop_transcripts30.fa.txt Molgula-occidentalis_Blue 005_moxi-maker2.all.maker.proteins_goodNomenclature_filtered.aa 005_moxi-maker2.all.maker.transcripts_goodNomenclature_filtered.fasta Molgula-oculata_Blue 005_PEP_M_oculata_maker2.all9_proteins_goodNomenclature_filtered.aa 005_CDS_M_oculata_maker2.all9_transcripts_goodNomenclature_filtered.fasta Ciona-savignyi_Blue 000_OnlyLongestPEP_Ciona_savignyi.CSAV2.0.pep.all.fa 000_OnlyLongestCDS_Ciona_savignyi.CSAV2.0.cds.all.fa Ciona-intestinalis_Blue 000_OnlyLongestPEP_Ciona_intestinalis.KH.pep.all.fa 000_OnlyLongestCDS_Ciona_intestinalis.KH.cds.all.fa >SpeciesTree [&r](Streptomyces-coelicolor,(Arabidopsis-thaliana,(Saccharomyces-cerevisiae,(Capsaspora-owczarzaki,((Salpingoeca-rosetta,Monosiga-brevicollis)Salpingoecidae,(Mnemiopsis-leidyi,(Amphimedon-queenslandica,(Trichoplax-adhaerens,(((Thelohanellus-kitauei,Hydra-vulgaris)MyxozoaHydrozoa,Acropora-digitifera)Cnidaria,(((Schistosoma-mansoni,(Capitella-teleta,((Notospermus-geniculatus,Phoronis-australis)NemerteaBrachiopoda,(Octopus-bimaculoides,(Biomphalaria-glabrata,(Crassostrea-gigas,Pinctada-fucata)Bivalvia)Conchifera)Mollusca)NotospermusMollusca)Trochozoa)Spiralia,(Priapulus-caudatus,((Trichinella-spiralis,Caenorhabditis-elegans)Nematoda,(Limulus-polyphemus,(Strigamia-maritima,(Hyalella-azteca,(Pediculus-humanus,(Zootermopsis-nevadensis,(Rhodnius-prolixus,(Nasonia-vitripennis,(Dendroctonus-ponderosae,(Bombyx-mori,Drosophila-melanogaster)LepidopteraDiptera)ColeopteraDiptera)HymenopteraDiptera)HemipteraDiptera)DictyopteraDiptera)Hexapoda)Pancrustacea)Mandibulata)Chelicerata)NematodaArthropoda)Ecdysozoa)Protostomia,(((Ptychodera-flava,Saccoglossus-kowalevskii)Hemichordata,(Acanthaster-planci,Strongylocentrotus-purpuratus)Echinodermata)Ambulacraria,((Branchiostoma-floridae,Branchiostoma-belcheri)Cephalochordata,((Oikopleura-dioica,(((Molgula-oculata,Molgula-occidentalis)Molgulidae,(Botryllus-schlosseri,Botrylloides-leachii)Styelidae)Stolidobranchia,(Salpa-thompsoni,(Ciona-intestinalis,Ciona-savignyi)Enterogona)ThaliaceaEnterogona)Ascidiacea)Urochordata,(Homo-sapiens-E102,Gallus-gallus-E102)Vertebrata)Olfactore)Chordata)Deuterostomia)Bilateria)CnidariaBilateria)PlacozoaBilateria)PoriferaBilateria)Metazoa)SalpingoecidaeMetazoa)Holozoa)Opisthokonta)Eukaryota)LUCA; >SpeciesWithGeneFunction Ciona-intestinalis # Number of rooting sequences >Num_rootSequences 1 # This species node is used to find orthogroups within gene trees. >OrthogroupBasalNode Bilateria # Floating point expression such as 1e-3 and 1e-5, or just 1 >BLAST_Evalue_threshold_for_reported_sequences 1e-3 >Number_of_hits_to_report_per_genome 10 # This fraction is used to evaluate short sequences that interferes with tree searchs. >ShortSequence_threshold 0.45 # Exclude3rd, Include3rd, or AminoAcid >Dataset Exclude3rd >RearrangementBSthreshold 60 >Outdir /flash/SatohU/inoue/orthoscopeStar/outdir_CesA0429_bilateriaBH10 >Database database # L: Leave intermediate process # D: Delete these files >Switch_deleteIntermediateFiles D