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biology/paml/pkg-descr
Phylogenetic Analysis by Maximum Likelihood (PAML) | Phylogenetic Analysis by Maximum Likelihood (PAML) | ||||
PAML is a program package for phylogenetic analyses of DNA or protein | PAML is a package of programs for phylogenetic analyses of DNA or protein | ||||
sequences using maximum likelihood, and is maintained and distributed | sequences using maximum likelihood. It is not good for tree making. It may be | ||||
by Ziheng Yang. | used to estimate parameters and test hypotheses for the study the evolutionary | ||||
process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY, | |||||
Possible uses of the programs are: | PhyML, or RaxML. | ||||
- 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. | |||||
WWW: http://abacus.gene.ucl.ac.uk/software/paml.html | WWW: http://abacus.gene.ucl.ac.uk/software/paml.html |