马尔科夫蒙特卡洛
系统发育树
分子钟
分子系统发育学
分子进化
贝叶斯概率
多序列比对
进化生物学
成对比较
最大节俭
序列(生物学)
分歧(语言学)
系统发育学
计算生物学
生物
计算机科学
序列比对
人工智能
遗传学
克莱德
基因
语言学
哲学
肽序列
出处
期刊:Oxford University Press eBooks
[Oxford University Press]
日期:2014-05-15
被引量:221
标识
DOI:10.1093/acprof:oso/9780199602605.001.0001
摘要
Abstract This book summarizes the statistical models and computational algorithms for comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, and statistical phylogeography. The book presents and explains the models of nucleotide, amino acid, and codon substitution, and their use in calculating pairwise sequence distances and in reconstruction of phylogenetic trees. All major methods for phylogeny reconstruction are covered in detail, including neighbour joining, maximum parsimony, maximum likelihood, and Bayesian methods. Using motivating examples, the book includes a comprehensive introduction to Bayesian computation using Markov chain Monte Carlo (MCMC). Advanced topics include estimation of species divergence times using the molecular clock, detection of molecular adaptation, simulation of molecular evolution, as well as species tree estimation and species delimitation using genomic sequence data.
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