HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction | Zendy

Oscar Westesson | Zendy; Lars Barquist | Zendy; Ian Holmes | Zendy

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HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

Author(s) -

Oscar Westesson,

Lars Barquist,

Ian Holmes

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts058

Subject(s) - markov chain monte carlo , computer science , bayesian probability , multiple sequence alignment , bayesian inference , sequence (biology) , phylogenetic tree , inference , metropolis–hastings algorithm , indel , sampling (signal processing) , algorithm , artificial intelligence , sequence alignment , biology , genetics , genotype , single nucleotide polymorphism , peptide sequence , gene , filter (signal processing) , computer vision

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.

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