RERconverge

RERconverge associates relative evolutionary rates of genes with convergent traits across phylogenies to identify genes exhibiting convergent evolutionary rate shifts and link them to binary or continuous trait evolution.

Key Features:

• Detection of convergent evolutionary rate shifts: Tests for associations between relative evolutionary rates of genes and traits that have evolved across a phylogeny to identify genes with signatures of convergent rate shifts.
• Trait flexibility: Supports analyses of both binary and continuous traits.
• Visualization tools: Provides functions to visualize the results of association tests.
• Enrichment analyses: Performs enrichment analyses on genes identified by association tests to detect overrepresented biological processes or pathways.

Scientific Applications:

• Identifying genetic bases of convergent traits: Detects genes whose evolutionary rates correlate with convergent phenotypes across independent lineages.
• Elucidating molecular mechanisms of convergent evolution: Prioritizes genes and pathways repeatedly targeted by selection in convergent adaptations.
• Comparative genomic analyses across taxa: Applicable to studies in diverse organisms, including mammals, Drosophila, and yeast, to investigate trait-associated rate shifts.

Methodology:

Performs association tests between relative evolutionary rates of genes and traits across a phylogeny, supports binary and continuous trait models, conducts enrichment analyses on association results, and generates visualizations of association test outputs.