# the number of species you want to be included in each analysis
nways: 3
# How you want to identify the orthologs [diamond|blastp]
search_method: blast
num_permutations: 100000000
rbh_file: odp_nway_rbh/step1-rbh/Bfloridae_Hvulgaris_Myessoensis_reciprocal_best_hits.rbh
# What analyses you want to produce. Saves on some compute.
# Must match headers of `xaxisspecies`. Order doesn't matter.
analyses:
  - ["Hvulgaris", "Bfloridae", "Myessoensis"]
  # - ["Homosapiens", "Dmel", "Mmus"]   # You can comment out lines if you would like
  
species:
  Hvulgaris:
    proteins: /home/FM/tcunha/nematomorpha-synteny/data/GCF_022113875.1_Hydra_105_v3_Hydra_vulgaris/GCF_022113875.1_Hydra_105_v3_protein.faa.gz
    chrom: /home/FM/tcunha/nematomorpha-synteny/data/GCF_022113875.1_Hydra_105_v3_Hydra_vulgaris/Hydra_vulgaris.chrom
    genome: /home/FM/tcunha/nematomorpha-synteny/data/GCF_022113875.1_Hydra_105_v3_Hydra_vulgaris/GCF_022113875.1_Hydra_105_v3_genomic.fna.gz
  Bfloridae:
    proteins: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000003815.2_Bfl_VNyyK_Branchiostoma_floridae/GCF_000003815.2_Bfl_VNyyK_protein.faa.gz
    chrom: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000003815.2_Bfl_VNyyK_Branchiostoma_floridae/Branchiostoma_floridae.chrom
    genome: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000003815.2_Bfl_VNyyK_Branchiostoma_floridae/GCF_000003815.2_Bfl_VNyyK_genomic.fna.gz
  Myessoensis:
    proteins: /home/FM/tcunha/nematomorpha-synteny/data/GCA_002113885.2_ASM211388v2_Patinopecten_yessoensis/GCF_002113885.1_ASM211388v2_protein.faa.gz
    chrom: /home/FM/tcunha/nematomorpha-synteny/data/GCA_002113885.2_ASM211388v2_Patinopecten_yessoensis/Mizuhopecten_yessoensis.chrom
    genome: /home/FM/tcunha/nematomorpha-synteny/data/GCA_002113885.2_ASM211388v2_Patinopecten_yessoensis/GCF_002113885.1_ASM211388v2_genomic.fna.gz
  Ppacificus:
    proteins: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000180635.4_El_Paco_v._4_Pristionchus_pacificus/GCA_000180635.4_El_Paco_v._4_protein.faa.gz
    chrom: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000180635.4_El_Paco_v._4_Pristionchus_pacificus/Pristionchus_pacificus.chrom
    genome: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000180635.4_El_Paco_v._4_Pristionchus_pacificus/GCA_000180635.4_El_Paco_v._4_genomic.fna.gz
  Dmelanogaster:
    proteins: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000001215.4_Release_6_plus_ISO1_MT_Drosophila_melanogaster/GCF_000001215.4_Release_6_plus_ISO1_MT_protein.faa.gz
    chrom: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000001215.4_Release_6_plus_ISO1_MT_Drosophila_melanogaster/Drosophila_melanogaster.chrom
    genome: /home/FM/tcunha/nematomorpha-synteny/data/GCA_000001215.4_Release_6_plus_ISO1_MT_Drosophila_melanogaster/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz