BAli-Phy

BAli-Phy is a software tool that uses Bayesian posterior sampling and Markov chain Monte Carlo to estimate the alignment and phylogeny of molecular sequence data. By simultaneously estimating alignment and phylogeny, BAli-Phy avoids bias toward inaccurate alignment guide-trees and employs more sophisticated substitution models during alignment. Additionally, BAli-Phy automatically utilizes information in shared insertion/deletions to help infer phylogenies.

Topic

Phylogenetics;Sequence analysis

Detail

  • Operation: Multiple sequence alignment;Phylogenetic tree generation (from molecular sequences);Phylogenetic tree generation (maximum likelihood and Bayesian methods)

  • Software interface: Command-line user interface

  • Language: ;Markov chain Monte Carlo software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming.;Command-line tool

  • License: -

  • Cost: Free

  • Version name: 4.0-beta2

  • Credit: NIH, NSF, USPHS

  • Input: -

  • Output: -

  • Contact: benjamin.redelings@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.
  • Suchard MA and Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. 2006; 22:2047-8. doi: 10.1093/bioinformatics/btl175
  • https://doi.org/10.1093/bioinformatics/btl175
  • PMID: 16679334
  • PMC: -

Download and documentation

< Back to DB search