PAML

PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Possible uses of the programs are:

• Estimation of branch lengths in a phylogenetic tree and parameters in the evolutionary model such as the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates among sites, and rate parameters for different genes; Test of hypotheses concerning sequence evolution, such as rate constancy and independence among nucleotide or amino acid sites, rate constancy among lineages (the molecular clock), and homogeneity of evolutionary process in multiple genes; Calculation of substitution rates at sites; Reconstruction of ancestral nucleotide or amino acid sequences; Simulation of nucleotide, codon, and amino acid sequence data sets; Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods .

Possible uses of the programs are:

•      baseml
•      ML analysis of nucleotide sequence
•      basemlg
•      ML analysis of nucleotide sequences under the model of gamma rates among sites.
•      codonml(codeml with seqtryp = l):
•      ML analysis of protein-coding DNA sequences using codon substitution models.
•      aaml(codeml with seqtryp = 2):
•      ML analysis of amino acid sequences under a number of amino acid substitution models.
•      pamp
•      Parsimony-based analyses for a given tree topology, estimation of the substitution pattern.
•      mcmctree
•      Bayesian estimation of phylogenies using DNA sequence data. Markov chain Monte Carlo calculation of                    posterior probabilities of trees.
•      evolver
•      This program used to be named listtree and does miscellaneous things.
•      yn00
•      This program implements the method of Yang and Nielsen (2000) for estimating synonymous and                      
•      nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.