PAML 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: http://abacus.gene.ucl.ac.uk/ziheng/paml.html 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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