title: HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.
abstract: 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.
  
  
  METHODS
  Installation and usage instructions are at http://biowiki.org/HandAlign.
authors.affiliation: Department of Bioengineering, University of California Berkeley, CA 94720, USA.
authors.forename: Oscar
authors.initials: O
authors.lastname: Westesson
authors.forename: Lars
authors.initials: L
authors.lastname: Barquist
authors.forename: Ian
authors.initials: I
authors.lastname: Holmes
mesh_terms: D001499:Bayes Theorem; D006678:HIV / Q000235:genetics; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D054643:INDEL Mutation; D008390:Markov Chains; D008562:Membrane Glycoproteins / Q000235:genetics; D009010:Monte Carlo Method; D010802:Phylogeny; D016415:Sequence Alignment; D015302:Simian Immunodeficiency Virus / Q000235:genetics; D012984:Software; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D015699:HIV Envelope Protein gp120; D008562:Membrane Glycoproteins; D014759:Viral Envelope Proteins; C069623:gp120 protein, Simian immunodeficiency virus