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.

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