forester

forester infers speciation and gene duplication events by reconciling gene trees with a trusted species tree to identify orthologs and support phylogenomic functional prediction.

Key Features:

• Automated phylogenomic analysis: Automates genome annotation and functional prediction using explicit phylogenetic trees and inferred orthology relationships.
• Speciation and duplication event inference: Infers speciation and gene duplication events by comparing gene trees against a trusted species tree to distinguish orthologs from paralogs.
• Algorithmic efficiency: Implements an algorithm with a theoretical worst-case running time of O(n(2)) while often performing effectively and competitively with algorithms of approximate complexity O(n) except in pathological cases.
• Implementation: Provided as Java and Ruby libraries for programmatic use in computational workflows.
• Empirical validation: Validated using 1,750 gene trees constructed from the Pfam protein family database.

Scientific Applications:

• Genome annotation: Enables phylogeny-based assignment of gene function to improve annotation accuracy.
• Protein function prediction: Supports more reliable protein function prediction through identification of orthologous sequences.
• Evolutionary biology: Facilitates analysis of speciation and duplication patterns across gene families for evolutionary studies.
• Therapeutic target research: Aids identification of functionally conserved proteins that can inform therapeutic target discovery.

Methodology:

Compares gene trees with a trusted species tree to infer speciation and duplication events using the stated reconciliation algorithm, whose theoretical worst-case complexity is O(n(2)) but which has shown practical effectiveness.