Supplementary Material for poppr 2.0 manuscript

This repository contains supplemental materials relating to the manuscript submitted to Frontiers called "Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality" By Zhian N. Kamvar (@zkamvar), Jonah C. Brooks (@JonahBrooks), and Niklaus J. Grünwald (@grunwald).

Citation

Please cite this supplementary material as:

ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'. DOI: 10.5281/zenodo.17424

Setup

To use the scripts in this repository, you will need the latest versions of poppr and adegenet.

From a unix shell:

make boot

From within R:

local({r <- getOption("repos"); r["CRAN"] <- "http://cran.at.r-project.org"; options(repos = r)})
install.packages(c("ape", "knitr", "rmarkdown", "animation", "devtools"))
devtools::install_github(c("thibautjombart/adegenet", "emmanuelparadis/pegas/pegas", "KlausVigo/phangorn"))

devtools::install_github("grunwaldlab/poppr@2.0-rc")

Folders

Rscripts

The folder called Rscripts contain R scripts, corresponding HTML files, and cached information used for the manuscript and supplementary information. Please see Rscritps/README for more details.

Images

The folder called images contains HTML animations of dendrograms collapsing multilocus genotypes by genetic distance.