PAML

PAML is a tool package for reconstructing and fitting models of phylogenetic trees. The PAML algorithm uses the Maximum Likelihood (ML) method.

Topic

Phylogenetics;Sequence analysis

Detail

Operation: Probabilistic sequence generation;Phylogenetic tree generation (maximum likelihood and Bayesian methods);Phylogenetic tree analysis
Software interface: Command-line user interface;Graphical user interface
Language: C
License: GNU General Public License v3.0
Cost: Free
Version name: 4.10.5
Credit: Case Western Reserve University.
Input: -
Output: -
Contact: -
Collection: --
Maturity: -

Publications

PAML: a program package for phylogenetic analysis by maximum likelihood.
Yang Z (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13(5): 555-6.
https://doi.org/10.1093/bioinformatics/13.5.555
PMID: 9367129
PMC: -

PAML 4: phylogenetic analysis by maximum likelihood.
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007 Aug;24(8):1586-91. doi: 10.1093/molbev/msm088. Epub 2007 May 4. PMID: 17483113.
https://doi.org/10.1093/molbev/msm088
PMID: 17483113
PMC: -

Download and documentation

Source: https://github.com/abacus-gene/paml/releases/tag/v4.10.5
Documentation: https://github.com/abacus-gene/paml/tree/master/doc
Home page: http://abacus.gene.ucl.ac.uk/software/paml.html
Links: https://github.com/abacus-gene/paml/tree/master/examples

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