orthofisher

orthofisher identifies single-copy orthologs by aligning query Hidden Markov Model (HMM) profiles against proteome datasets to support phylogenomic and evolutionary analyses.

Key Features:

• Automated Identification: Automates identification of orthologous genes by aligning query HMM profiles against proteomes and retrieving matching protein sequences.
• High Accuracy and Precision: Demonstrates high accuracy and precision in identifying single-copy orthologs based on performance assessment.
• Versatile Applications: Applies to assessing gene annotation quality, identifying single-copy orthologs for phylogenomic studies, estimating gene copy numbers across species, and conducting evolutionary analyses dependent on accurate homolog identification.

Scientific Applications:

• Phylogenomics: Identifies single-copy orthologs for constructing phylogenetic trees and comparative genomic analyses.
• Gene copy number estimation: Enables estimation of gene family copy numbers across multiple species using retrieved orthologs.
• Gene annotation quality assessment: Assesses completeness and quality of gene annotations by detecting expected orthologs.
• Evolutionary analyses: Supports evolutionary studies that require accurate homologous gene identification.

Methodology:

Leverages Hidden Markov Model (HMM) profile alignments by aligning query HMM profiles against a set of proteomes to retrieve genes with high sequence similarity and identify single-copy orthologs.