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PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. 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

Home Site:

Source Code Availability:   Yes

Available Binary Packages:

  • Debian Package:   No
  • RedHat RPM Package:   No
  • Other Packages:   No

Targeted Platforms:

ANSI C Platform, PowerMAC and Windows 95/NT executables are available

Software/Hardware Requirements:

ANSI C Compiler, such as gcc. Compiled fine on Linux/gcc

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