Software

smartsnp

smartsnp is an R package for multivariate analysis (PCA, PERMANOVA, PERMDISP) of large-scale genetic variation data. It also allows for the projection of ancient DNA into PCA space computed from modern data.

predicDiv 

(hosted by Lohmueller group)

Infer Divergence using DFE and Demography. Scripts associated with Zhen et al 2020. 

SweepFinder2 

(hosted by DeGiorgio group)

A program written in C that can perform genomic scans for recent selective sweeps selection while controlling for background selection and mutation rate variation.

fitdadi 

(hosted by Lohmueller group)

Tools for inference of the distribution of fitness effects (DFE) from large sample-size data with dadi.

Dominance inference 

(hosted by Lohmueller group)

Scripts for Huber, Durvasula, Hancock, and Lohmueller 2017.