pegi3s/paml

Sponsored OSS

By i3S

Updated over 3 years ago

PAML (http://abacus.gene.ucl.ac.uk/software/paml.html) docker image.

Image
Data Science
Machine Learning & AI

717

This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

This image facilitates the usage of PAML (Phylogenetic Analysis by Maximum Likelihood), a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Using the PAML image in Linux

Note: Most programs in the PAML package have control files that specify the names of the sequence data file, the tree structure file, and models and options for the analysis. The default control files are baseml.ctl for baseml and basemlg, codeml.ctl for codeml, pamp.ctl for pamp, mcmctree.ctl for mcmctree. You must change these control files accordingly.

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/paml /data/control_file

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the input files you want to analyze.
  • control_file to the actual name of the control file you want to run.

For instance, to run the control file for codeml you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/paml /data/codeml.ctl

Docker Pull Command

docker pull pegi3s/paml