pegi3s/phipack 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 PhiPack⁠ software. PhiPack implements tests for recombination (Pairwise Homoplasy Index (Phi), Maximum χ2 (Max Chi^2) and the Neighbour Similarity Score (NSS)), and can produce refined incompatibility matrices.

⁠Using the PhiPack image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/phipack bash -c "Phi -f /data/input.fasta -p 1000 -o > /data/output"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the aligned FASTA file you want to analyze.
• input.fasta to the actual name of your input file.
• output to the actual name of your output file.

To see the PhiPack help, just run docker run --rm pegi3s/phipack Phi.