extract sequences based on the results of OrthoFinder (orthogroup)
rubygenerateAlnFromOrthoFinder.rb
--force remove outdir if it exists, and create a new one
--suffix extention of input sequences
--count_min_max_total min and max no. of genes total (example: 90,100)
--count_min_max_per_taxon min and max no. of genes per taxon (example: 0,1)
--include_list only consider the taxa on the list
--print_taxon delete gene locus name
ruby generateAlnFromOrthoFinder.rb --seq_indir pep --orthogroup Orthogroups.tsv --outdir out-pep --cpu 2 --force --suffix fas --count_min_max_total 10,10 --count_min_max_per_taxon 1,1 --include_list include.list --print_taxon
Assuming that you have 10 genomes, --count_min_max_total 10,10 --count_min_max_per_taxon 1,1 will help you retrieve all strict single copy genes. "--count_min_max_total 9,10 --count_min_max_per_taxon 0,1" will retrieve all single copy genes absent in at most one genomes.