rbrothers

rbrothers detects phylogenetic recombination by applying a Bayesian multiple change-point model to identify changes in phylogenetic signal across sequence segments.

Key Features:

• Integration with R: Provides functions within the R environment for analysis of molecular sequence and phylogenetic data.
• Bayesian multiple change-point model: Implements a Bayesian multiple change-point model to infer recombination breakpoints by detecting shifts in phylogenetic relationships.
• Pre-processing of input trees: Includes routines to prepare input phylogenetic trees required by the multiple change-point model.
• Post-processing tools: Offers Markov chain Monte Carlo (MCMC) convergence diagnostics and routines to generate result summaries and visualizations.
• Comparative analysis application: Has been applied to analyze recombination in fimA and fimH genes encoding type 1 fimbriae from Salmonella enterica.

Scientific Applications:

• Phylogenetic recombination detection: Integrates recombination detection into phylogenetic workflows within R to study evolutionary processes and molecular genetics.
• Comparative gene analysis: Enables investigation of recombination and evolutionary relationships in genes such as fimA and fimH from Salmonella enterica.

Methodology:

Bayesian inference using a multiple change-point model with MCMC sampling; pre-processing to prepare input phylogenetic trees; post-processing for MCMC convergence diagnostics and result summaries and visualizations.