Orthofisher: a broadly applicable tool for automated gene identification and retrieval.

Abstract

Identification and retrieval of genes of interest from genomic data are an essential step for many bioinformatic applications. We present orthofisher, a command-line tool for automated identification and retrieval of genes with high sequence similarity to a query profile Hidden Markov Model sequence alignment across a set of proteomes. Performance assessment of orthofisher revealed high accuracy and precision during single-copy orthologous gene identification. orthofisher may be useful for assessing gene annotation quality, identifying single-copy orthologous genes for phylogenomic analyses, estimating gene copy number, and other evolutionary analyses that rely on identification and retrieval of homologous genes from genomic data. orthofisher comes complete with comprehensive documentation (https://jlsteenwyk.com/orthofisher/), is freely available under the MIT license, and is available for download from GitHub (https://github.com/JLSteenwyk/orthofisher), PyPi (https://pypi.org/project/orthofisher/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/orthofisher).