pegi3s/paml
PAML (http://abacus.gene.ucl.ac.uk/software/paml.html) docker image.
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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.
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 pegi3s/paml