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PAML

PAML is a suit of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. The bundle packages version 4.10.7.

Usage example

The following command can be executed in the terminal to load the bundle:

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module load paml

The module makes the following commands available:

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baseml
basemlg
chi2
codeml
evolver
mcmctree
pamp
yn00

The paml_shell command can be used to access a shell in the bundle.

The PAML commands use control files, therefore, no command line examples are provided.

Performance notes

No performance notes available

PAML should be run on a system with at least 4 GB of RAM and 1 threads.

Benchmarks

No benchmarks available.

Community guides and tutorials

  • No community guides available.

Official site and documentation

Licensing information

PAML is licensed under the GPLv3 license.

Primary citation

Yang, Z (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591. PMID: 17483113 doi

External guides and resources

  • If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za