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A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
23 lines
1.1 KiB
Plaintext
23 lines
1.1 KiB
Plaintext
Phylogenetic Analysis by Maximum Likelihood (PAML)
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PAML is a program package for phylogenetic analyses of DNA or protein
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sequences using maximum likelihood, and is maintained and distributed
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by Ziheng Yang.
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Possible uses of the programs are:
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- Estimation of branch lengths in a phylogenetic tree and parameters
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in the evolutionary model such as the transition/transversion rate
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ratio, the shape parameter of the gamma distribution for variable
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evolutionary rates among sites, and rate parameters for different
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genes;
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- Test of hypotheses concerning sequence evolution, such as rate
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constancy and independence among nucleotide or amino acid sites, rate
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constancy among lineages (the molecular clock), and homogeneity of
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evolutionary process in multiple genes;
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- Calculation of substitution rates at sites;
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- Reconstruction of ancestral nucleotide or amino acid sequences;
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- Simulation of nucleotide, codon, and amino acid sequence data sets;
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- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.
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WWW: http://abacus.gene.ucl.ac.uk/software/paml.html
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