The treeWAS R package allows users to apply our phylogenetic tree-based appraoch to Genome-Wide Association Studies (GWAS) to microbial genetic and phenotypic data. In short, treeWAS measures the statistical association between a phenotype of interest and the genotype at all loci, with the aim of identifying significant associations, while correcting for the confounding effects of clonal population structure and homologous recombination. treeWAS is applicable to both bacterial and viral genetic data from both the core and accessory genomes, and to both binary and continuous phenotypes.The approach adopted within treeWAS is described fully in our paper, available in PLOS Computational Biology.

treeWAS is currently hosted on GitHub at https://github.com/caitiecollins/treeWAS.

The most up-to-date version of treeWAS can be easily installed directly within R, using the devtools package:

## install devtools, if necessary:
install.packages("devtools", dep=TRUE)
library(devtools)

## install treeWAS from github:
install_github("caitiecollins/treeWAS", build_vignettes = TRUE)
library(treeWAS)

Documentation on how to use treeWAS can be found on GitHub in the Wiki.

The Wiki contains sections on The Method behind treeWAS, the Data & Data Cleaning required, the treeWAS Function & Arguments, a guide to Interpreting Output returned by treeWAS, functions to facilitate Integration with ClonalFrameML, and information describing how to flag Bugs & Features.

Once you have installed and loaded the treeWAS package, you can also find this information in the vignette. To open the vignette from within R (recommended if any formatted elements are not rendering properly in the wiki), run browseVignettes and click on the HTML hyperlink:

browseVignettes("treeWAS")

You may also find useful tips and relevant discussions among the Issues posted by other users (including Closed Issues).