BYPASSR

BYPASSR infers phylogenetic branch lengths and site-specific nucleotide substitution rates using Bayesian Markov Chain Monte Carlo methods applied to continuous-time Markov substitution models.

Key Features:

• Bayesian MCMC Estimation: Estimates branch lengths and site-specific substitution rates using Bayesian Markov Chain Monte Carlo (MCMC) algorithms.
• Uniformization-Based Computation: Applies uniformization techniques to transform continuous-time Markov substitution processes into Poisson substitution processes with discrete state transitions.
• General Time Reversible Model Support: Implements complex nucleotide substitution models including the General Time Reversible (GTR) model.
• Gamma-Distributed Rate Modeling: Models site-specific substitution rates using a continuous gamma distribution.

Scientific Applications:

• Phylogenetic Branch Length Estimation: Estimates evolutionary branch lengths from nucleotide sequence alignments.
• Site-Specific Evolutionary Rate Analysis: Identifies variation in substitution rates across nucleotide sites.
• Molecular Evolution Studies: Detects evolutionary patterns such as negative and positive selection across codon positions.

Methodology:

BYPASSR applies Bayesian Markov Chain Monte Carlo inference with uniformization to convert continuous-time Markov substitution models, such as the GTR model with gamma-distributed rates, into Poisson substitution processes for estimating branch lengths and site-specific substitution rates.