OrthoFinder

OrthoFinder infers orthogroups and orthologs across multiple species to enable comparative genomics and evolutionary analysis.

Key Features:

• Orthogroup inference algorithm: Implements a novel orthogroup inference algorithm that has been empirically validated on benchmark datasets.
• Gene length bias correction: Resolves a previously undetected gene length bias in orthogroup inference to improve precision of homology relationships.
• Benchmark accuracy: Demonstrates an accuracy improvement of 8% to 33% over other orthogroup inference methods on real benchmark datasets.
• Rooted gene tree inference: Infers rooted gene trees for all identified orthogroups.
• Duplication detection and mapping: Identifies gene duplication events within gene trees and maps those events onto a rooted species tree.
• Gene family classification: Provides comprehensive classifications of complex gene families, including transcription factor gene families in plants, revealing 6.9 million previously unobserved relationships.

Scientific Applications:

• Comparative genomics: Infers orthologs and orthogroups to support cross-species genomic comparisons.
• Evolutionary history reconstruction: Traces gene duplication events and maps them onto species trees to study gene and species evolution.
• Gene family analysis: Classifies complex gene families (e.g., plant transcription factor families) and uncovers novel intra-family relationships.

Methodology:

Infers rooted gene trees for all orthogroups, identifies gene duplication events within those gene trees, maps duplications onto a rooted species tree, and applies an orthogroup inference algorithm that corrects gene length bias and was benchmarked on real datasets showing 8%–33% accuracy improvement.