PAML 4.7

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

Website: http://abacus.gene.ucl.ac.uk/software/paml.html

Downloads

Installation

Extract the files in your home directory.

$gzip -d paml4.tar.gz
$tar xf paml4.tar

Delete all Windows executables and compile the files in the directory paml41.

$ls -lF bin
$rm -r bin/*.exe
$cd src
$make
$rm *.o
$mv baseml basemlg codeml pamp evolver yn00 chi2 ../bin

The PAML is now installed.

Input files

Are required three input files:

  1. Control file (*.ctl)
    containing the parameters that will be used in analysis
  2. Sequence file (*.seq)
    Your profile containing the sequence alignment in PHYLIP format. It can be generated by DNAsp software. Note: Stop codon is not acceptable in PAML.
  3. Tree file (*.tree)
    Phylogenetic tree from your sequences in NEWICK format. If you perform a Bayesian phylogenetic tree using MrBayes software, the NEWICK tree can be generated by FigTree software with the ‘tree.con’ as input file.

Executing PAML softwares

To execute some software from PAML package, copy all three input files to inside of software directory created on Installation step.
If you want to execute the codeml software, copy the three input files to directory /home/paml41/codeml.

Next, execute the software by typing:

./codeml

For extensively and more detailed information, you can download the work performed by Lynn (2007).

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