# E: Estimate gene trees, orthogroup members, etc.
# D: Draw phylogenetic trees.
# S: Summarize results.
>Mode
E

>QuerySpecies
Oryzias-latipes

# SpaciesName_color                 Amino acide database                                                                           Nucleotide database
>TaxonSampling
Drosophila-melanogaster_Black       000_OnlyLongestPepsTranslated_Drosophila_melanogaster.BDGP6.cds.pep.all.fa.txt                  000_OnlyLongestCDStrans_Drosophila_melanogaster.BDGP6.cds.all.fa.txt
Acanthaster-planci_Black            000_OnlyLongestPEP_Acanthaster-planci_oki-cotsv1.0.EVM2a.prot.txt                               000_OnlyLongestCDS_Acanthaster-planci_oki-cotsv1.0.EVM2a.mrna.txt
Branchiostoma-floridae_Black        000_OnlyLongestPEP_B-floridae_GCF_000003815.1_Version_2_rna.gbff.txt                            000_OnlyLongestCDS_B-floridae_GCF_000003815.1_Version_2_rna.gbff.txt
Xenopus-tropicalis_Magenta          000_OnlyLongestPEP_Xenopus_tropicalis.JGI_4.2.pep.all.fa                                        000_OnlyLongestCDS_Xenopus_tropicalis.JGI_4.2.cds.all.fa
Anolis-carolinensis_Magenta         000_OnlyLongestPEP_Anolis_carolinensis.AnoCar2.0.pep.all.fa                                     000_OnlyLongestCDS_Anolis_carolinensis.AnoCar2.0.cds.all.fa
Gallus-gallus_Magenta               000_OnlyLongestPEP_Gallus_gallus-E102.GRCg6a.pep.all.fa.txt                                     000_OnlyLongestCDS_Gallus_gallus-E102.GRCg6a.cds.all.fa.txt
Homo-sapiens_Magenta                000_OnlyLongestPEP_Homo_sapiens-E102.GRCh38.pep.all.fa.txt                                      000_OnlyLongestCDS_Homo_sapiens-E102.GRCh38.cds.all.fa.txt
Acipenser-ruthenus_Purple           000_OnlyLongestPEP_prot_A-ruthenus_GCF_010645085.1_ASM1064508v1_rna.gbff.txt                    000_OnlyLongestCDS_nucl_A-ruthenus_GCF_010645085.1_ASM1064508v1_rna.gbff.txt
Lepisosteus-oculatus_Purple         000_OnlyLongestPEP_Lepisosteus_oculatus.LepOcu1.pep.all.fa                                      000_OnlyLongestCDS_Lepisosteus_oculatus.LepOcu1.cds.all.fa
Pangasianodon-hypophthalmus_Green   000_OnlyLongestPEP_prot_Pangasianodon-hypophthalmus_GCF_003671635.1_VN_pangasius_rna.gbff.txt   000_OnlyLongestCDS_nucl_Pangasianodon-hypophthalmus_GCF_003671635.1_VN_pangasius_rna.gbff.txt
Danio-rerio_Green                   000_OnlyLongestPEP_Danio_rerio.GRCz10.pep.all.fa                                                000_OnlyLongestCDS_Danio_rerio.GRCz10.cds.all.fa
Esox-lucius_Red                     000_OnlyLongestPEP_Esox-lucius_rna.gbk.txt                                                      000_OnlyLongestCDS_Esox-lucius_rna.gbk.txt
Oncorhynchus-kisutch_Red            000_OnlyLongestPEP_Oncorhynchus-kisutch_rna.gbk.txt                                             000_OnlyLongestCDS_Oncorhynchus-kisutch_rna.gbk.txt
Tetraodon-nigroviridis_Blue         000_OnlyLongestPEP_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.txt                             000_OnlyLongestCDS_Tetraodon_nigroviridis.TETRAODON8.cds.all.fa.txt
Oryzias-latipes_Blue                000_OnlyLongestPEP_Oryzias_latipes.MEDAKA1.pep.all.fa                                           000_OnlyLongestCDS_Oryzias_latipes.MEDAKA1.cds.all.fa

>SpeciesTree
(Drosophila-melanogaster,(Acanthaster-planci,(Branchiostoma-floridae,((Xenopus-tropicalis,((Anolis-carolinensis,Gallus-gallus)Sauria,Homo-sapiens)Amniota)Tetrapoda,(Acipenser-ruthenus,(Lepisosteus-oculatus,((Pangasianodon-hypophthalmus,Danio-rerio)Otophysi,((Esox-lucius,Oncorhynchus-kisutch)Protacanthopterygii,(Tetraodon-nigroviridis,Oryzias-latipes)Percomorpha)Euteleostei)Teleostei)Neopterygii)Actinopterygii)BonyVertebrates)Chordata)Deuterostomia)Bilateria;

>SpeciesWithGeneFunction
Homo-sapiens


# Number of rooting sequences
>Num_rootSequences
1

# This species node is used to find orthogroups within gene trees.
>OrthogroupBasalNode
BonyVertebrates

# 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
70

>Outdir
/flash/SatohU/inoue/orthoscopeStar/outdir0412

>Database
database

# L: Leave intermediate process
# D: Delete these files
>Switch_deleteIntermediateFiles
D