forest_popgen

A docker repo of Linux & R packages for the analysis of population genetics data.

Available to download from Docker hub.

Software package list (not exhaustive)

Genetic diversity analysis

adegenet, poppr, pegas, hierfstat, Arlequin, genepop

Genetic differentiation - hybridisation - assignment

Structure, Structure_threader, CLUMPAK, TreeMix, OpM, assignPOP

Signals of selection

Bayescan, OutFLANK, pcadapt, FDist (via Arlequin)

Phylogenetics

ape, phytools, ggtree

R packages for data cleaning, visualization, etc

tidyverse, ggplot2 helpers (ggThemeAssist, ggpubr, gghalves)

For a full software list, please have a look at the included Dockerfile.