Phylogenetic Analysis by Maximum Likelihood (PAML)
Introduction
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. 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.
This document is about downloading and compiling PAML and getting started. See the manual for more information about running programs in the package.
PAML Resources on the web
- PAML discussion group (Old posts are at the Genetics Software Forum)
- Redhat linux rpm in the Biorpms repository
- ML estimation of dN and dS on the web
- Joe Bielawski provided a PAML demo. See the data files and demo for the book chapter by Bielawski & Yang, 2005.
- A step-by-step manual for MCMCtree with an example dataset (MCMCtree.example.tgz) (the manual in English, Japanese, and Chinese)
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