PAML
documentation

Version 4 (July 2007)
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.

• UNIX
• Linux
• Mac OSX
• executables are provided for MS Windows

• DNA Sequences
• Protein Sequences

• PHYLIP (sequential and interleaved)
• limited support for the NEXUS

• Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood Computer Applications in BioSciences 13:555-556.
• Yang, Z. 2007. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586-1591 (http://abacus.gene.ucl.ac.uk/software/paml.html).