pegi3s/phipack
PhiPack (https://www.maths.otago.ac.nz/~dbryant/software/phimanual.pdf) docker image.
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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.
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 pegi3s/phipack