orthofisher

Orthofisher is a versatile command-line tool designed for the automated identification and retrieval of genes with high sequence similarity across a set of proteomes, utilizing query profile Hidden Markov Model (HMM) sequence alignments. It stands out for its high accuracy and precision, particularly in identifying single-copy orthologous genes, making it an invaluable asset for various bioinformatic applications. These include assessing the quality of gene annotations, identifying single-copy orthologous genes for phylogenomic analyses, estimating gene copy numbers, and conducting other evolutionary studies that depend on precisely identifying and retrieving homologous genes from genomic data.

Topic

Phylogenomics;Proteomics;Gene and protein families;Sequence sites, features and motifs;Model organisms

Detail

  • Operation: Data retrieval;Database search;Homology-based gene prediction

  • Software interface: Command-line interface

  • Language: Python

  • License: The MIT License

  • Cost: Free with restrictions

  • Version name: -

  • Credit: The Howard Hughes Medical Institute (through the James H. Gilliam Fellowships for Advanced Study program), the National Science Foundation, the National Institutes of Health/National Institute of Allergy and Infectious Diseases, the Guggenheim Foundation, and the Burroughs Wellcome Fund.

  • Input: -

  • Output: -

  • Contact: Jacob L Steenwyk jacob.steenwyk@vanderbilt.edu ,Antonis Rokas antonis.rokas@vanderbilt.edu

  • Collection: -

  • Maturity: -

Publications

  • orthofisher: a broadly applicable tool for automated gene identification and retrieval.
  • Steenwyk JL and Rokas A. orthofisher: a broadly applicable tool for automated gene identification and retrieval. orthofisher: a broadly applicable tool for automated gene identification and retrieval. 2021; 11:(unknown pages). doi: 10.1093/g3journal/jkab250
  • https://doi.org/10.1093/G3JOURNAL/JKAB250
  • PMID: 34544141
  • PMC: PMC8496211

Download and documentation

< Back to DB search