pegi3s/paml repository overview

⁠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

⁠Using the PAML image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/paml /data/control_file