Modules

Every module is installed separately — none comes with the pipeline, and a fresh installation has an empty store. These are the ones published alongside this release, each on its own timetable and at its own version, installed with PoolSeqFlow analysis modules install <name> and documented here so you can read what one computes before deciding to install it.

Module	What it computes	Needs
verify	Reports what the analysis layer can see of your project, and produces nothing. Run it first when something is not being found	nothing
basicstats	Site counts, depth, effective pool size and gene diversity, per pool	the frequency and depth tables
association	Each allele's frequency against a phenotype you measured per pool, with a permutation p	the depth tables, and a pt_ column
mds	Every pool placed as a point, by Nei's minimum distance corrected for sampling	the depth tables

Run one at a time, from your project directory:

cd /path/to/project
PoolSeqFlow analysis basicstats

Each has a page of its own here. What comes first is what they have in common.