HandAlign：贝叶斯多序列比对、系统发育和祖先重建。
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.
机构信息
Department of Bioengineering, University of California Berkeley, CA 94720, USA.
出版信息
Bioinformatics. 2012 Apr 15;28(8):1170-1. doi: 10.1093/bioinformatics/bts058. Epub 2012 Jan 28.
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.
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我们描述了 handalign，这是一个用于贝叶斯重建系统发育历史的软件包。序列进化的基础模型描述了插入和替换。对齐、树和模型参数都被视为联合依赖的随机变量，并通过 Metropolis-Hastings 马尔可夫链蒙特卡罗（MCMC）进行采样，从而能够进行系统的统计参数推断和假设检验。handalign 实现了几种不同的 MCMC 提议内核，允许通过 Hastings 比率从任意目标分布进行采样，并使用标准文件格式用于树、对齐和模型。
可用性和实现
安装和使用说明在 http://biowiki.org/HandAlign。
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