PAML: Phylogenetic Analysis by Maximum Likelihood

PAML is a package of programs for phylogenetic analyses of DNA or
protein sequences using maximum likelihood. PAML is not good for tree
making. It may be used to estimate parameters and test hypotheses to
study the evolutionary process, when you have reconstructed trees
using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.

Notes about running of PAML programs and the package:

- Example datasets are included in /usr/share/paml/examples
- Control files for PAML programs are in /usr/share/paml
- Dcumentation can be found in /usr/doc/paml-$VERSION
- Additional executables are placed in /usr/libexec/paml

Suggested citation:
Yang, Z. 2007. PAML 4: a program package for phylogenetic analysis by
maximum likelihood. Molecular Biology and Evolution 24: 1586-1591
