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PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum
A summary of the types of analyses performed by different programs in the package is given below.
- baseml -- ML analysis of nucleotide sequences
- basemlg -- ML analysis of nucleotide sequences under the model gamma rates among sites.
- codonml (codeml with seqtype = 1) -- ML analysis of protein-coding DNA sequences using codon substitution models
- aaml (codeml with seqtype = 2) -- ML analysis of amino acid sequences under a number of amino acid substitution models
- pamp -- Parsimony-based analyses for a given tree topology
- mcmctree -- Bayesian estimation of phylogenies using DNA sequence data
- listtree -- listing all rooted and unrooted trees
for a given number of species, generating random trees with branch lengths from a birth-death
process with species sampling, calculating tree bipartition distances, etc.
Current Version: 1.4
License Type: Free for Academic Use
Source Code Availability: Yes
Available Binary Packages:
- Debian Package: No
- RedHat RPM Package: No
- Other Packages: No
ANSI C Platform, PowerMAC and Windows 95/NT executables are available
ANSI C Compiler, such as gcc. Compiled fine on Linux/gcc
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