geneplast

geneplast quantifies evolutionary plasticity and infers gene evolutionary roots from orthologous group distributions within species trees.

Key Features:

• Evolutionary Plasticity Index (EPI): Computes an Evolutionary Plasticity Index using Shannon information theory applied to ortholog abundance data to quantify gene adaptability.
• Bridge algorithm: Applies the Bridge algorithm to infer the evolutionary root of genes based on ortholog distribution across species.

Scientific Applications:

• Evolutionary biology: Analyze functional conservation and divergence of genes through orthologous group distributions.
• Comparative genomics: Quantify gene plasticity across species to study adaptive evolution using the EPI.
• Gene-environment interaction studies: Assess how genes may respond to environmental pressures by evaluating their EPI values.
• Phylogenomic root inference: Trace lineage and ancestral origins of genes using ortholog distribution and the Bridge algorithm.

Methodology:

Integrates orthologous group distribution data within species trees with Shannon information theory to compute the Evolutionary Plasticity Index (EPI) and applies the Bridge algorithm to determine gene evolutionary roots based on ortholog distribution.