Automated and high-throughout identification of a predetermined set of putative orthologous genes can be a helpful task for phylogenomics/phylogenetics, gene family copy number determination, etc.
To facilitate these analyses, orthofisher conducts automated HMMsearches among a set of proteomes using a predetermined set of orthologs. Sequence similarity searches classify results as multi-copy, single-copy, or absent in a given proteome. For the purposes of phylogenomics/phylogenetics, multi-fasta files are generated for all sequences as well as those that are single-copy; for gene family copy number determination, easily parsed output files contain absolute copy number of hits from the sequence similarity search.
If you found orthofisher useful, please cite orthofisher: a broadly applicable tool for automated gene identification and retrieval. Steenwyk & Rokas 2021, G3: Genes | Genomes | Genetics. doi: 10.1093/g3journal/jkab250.