Open Access
PAML: a program for package for phylogenetic analysis by maximum likelihood
About:
The article was published on 1997-01-01 and is currently open access. It has received 4896 citations till now.read more
Citations
More filters
Journal ArticleDOI
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Journal ArticleDOI
PAML 4: Phylogenetic Analysis by Maximum Likelihood
TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Journal ArticleDOI
The evolutionary fate and consequences of duplicate genes
Michael Lynch,John S. Conery +1 more
TL;DR: Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.
Journal ArticleDOI
HyPhy: hypothesis testing using phylogenies
TL;DR: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.
Journal ArticleDOI
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
Simon Whelan,Nick Goldman +1 more
TL;DR: The new model outperforms the Dayhoff and JTT models with respect to maximum-likelihood values for a large majority of the protein families in the authors' database and suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates.
References
More filters
Journal ArticleDOI
The rapid generation of mutation data matrices from protein sequences
TL;DR: An efficient means for generating mutation data matrices from large numbers of protein sequences is presented, by means of an approximate peptide-based sequence comparison algorithm, which is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fastenough to generate a matrix from a specific family or class of proteins in minutes.
Journal ArticleDOI
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
Nick Goldman,Ziheng Yang +1 more
TL;DR: Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio.
Journal ArticleDOI
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.
Ziheng Yang,Bruce Rannala +1 more
TL;DR: An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree, which has a probability of approximately 95%.
Journal ArticleDOI
Minimum mutation fits to a given tree
TL;DR: A method of generating all such minimum mutation fits is described, which is the assignment which permits representation of the data in a minimum number of symbols, which seems compelling in its own right.
Journal ArticleDOI
Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites.
Ziheng Yang,Sudhir Kumar +1 more
TL;DR: In this article, two approximate methods (one based on parsimony and one on pairwise sequence comparison) were proposed for estimating the pattern of nucleotide substitution and a parsimony-based method for estimating variable substitution rates among sites.