PhyKIT

PhyKIT processes and analyzes phylogenomic datasets to evaluate information content, infer evolutionary events, and predict gene functions from multiple sequence alignments (MSAs) and phylogenetic trees.

Key Features:

• Comprehensive function set: Contains 30 distinct functions for processing multiple sequence alignments (MSAs) and phylogenetic trees.
• Mutation rate estimation: Estimates mutation rates from sequence data.
• Sequence composition bias assessment: Evaluates sequence composition biases in MSAs.
• Molecular clock violation calculation: Calculates molecular clock violations.
• Low-support bipartition collapsing: Collapses low-support bipartitions (internal branches) in phylogenetic trees.
• Information content summarization: Summarizes information content of sequence alignments and trees to diagnose biases.
• Evolutionary rate covariation analysis: Evaluates gene–gene evolutionary rate covariation to identify functional relationships.
• Resolution and polytomy detection: Identifies lack of resolution events or polytomies in phylogenetic trees.

Scientific Applications:

• Bias diagnosis in sequence data: Detects and quantifies biases in MSAs and phylogenetic trees.
• Inference of evolutionary processes: Supports analysis of evolutionary events and molecular clock deviations using MSAs and trees.
• Functional prediction by covariation: Predicts gene functions and functional associations based on evolutionary rate covariation.
• Detection of rapid radiations or insufficient data: Identifies polytomies and low-resolution branches indicative of rapid diversification or limited signal.

Methodology:

Computational methods explicitly include estimation of mutation rates, assessment of sequence composition biases, calculation of molecular clock violations, collapsing low-support bipartitions, summarizing information content, computing evolutionary rate covariation among genes, and detecting polytomies.