HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.
Ontology highlight
ABSTRACT: Unlabelled
We describe handalign, a software package for Bayesian reconstruction of phylogenetic history. The underlying model of sequence evolution describes indels and substitutions. Alignments, trees and model parameters are all treated as jointly dependent random variables and sampled via Metropolis-Hastings Markov chain Monte Carlo (MCMC), enabling systematic statistical parameter inference and hypothesis testing. handalign implements several different MCMC proposal kernels, allows sampling from arbitrary target distributions via Hastings ratios, and uses standard file formats for trees, alignments and models.Availability and implementation
Installation and usage instructions are at http://biowiki.org/HandAlign.
SUBMITTER: Westesson O
PROVIDER: S-EPMC3324510 | biostudies-literature | 2012 Apr
REPOSITORIES: biostudies-literature
Publications
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.
Westesson Oscar O Barquist Lars L Holmes Ian I
Bioinformatics (Oxford, England) 20120128 8
<h4>Unlabelled</h4>We describe handalign, a software package for Bayesian reconstruction of phylogenetic history. The underlying model of sequence evolution describes indels and substitutions. Alignments, trees and model parameters are all treated as jointly dependent random variables and sampled via Metropolis-Hastings Markov chain Monte Carlo (MCMC), enabling systematic statistical parameter inference and hypothesis testing. handalign implements several different MCMC proposal kernels, allows ...[more]
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