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Introduction

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.

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• About
  • Performance Assessment
  • The Team
• Arguments
  • Required
  • Optional
• Install
  • 1) Prerequisite
  • 2) Install orthofisher
• Tutorial
  • 1) Creating HMMs
  • 2) Download the test data
  • 3) Run orthofisher
  • 4) Examine output
  • 5) Estimating gene family copy number
  • 6) Running orthofisher faster
• Change log
• Other software
  • ClipKIT
  • PhyKIT
  • treehouse
  • ggpubfigs
• FAQ

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