pegi3s/phipack

Sponsored OSS

By i3S

Updated 5 months ago

PhiPack (https://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf) docker image.

Image
Data Science
Machine Learning & AI

640

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.

Docker Pull Command

docker pull pegi3s/phipack