DMCA
Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods (1994)
| Venue: | J. Mol. Evol |
| Citations: | 536 - 28 self |
BibTeX
@ARTICLE{Yang94maximumlikelihood,
author = {Ziheng Yang},
title = {Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods},
journal = {J. Mol. Evol},
year = {1994},
volume = {39},
pages = {39--306}
}
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Abstract
Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the "discrete gamma model," uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous dis- tribution. The second method, called "fixed-rates mod- el," classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated.
Keyphrases
approximate method maximum likelihood phylogenetic estimation variable rate dna sequence star tree second method acceptable approximation discrete gamma model nucleotide site different class several category continuous dis tribution data set several class tree topology equal probability different characteristic near-optimum fit fixed-rates mod el gamma distribution
