WGPAN Whole-Genome Pairwise Alignment Noising

written by Bradford Condon, under advisement of Mark Farman University of Kentucky

Special thanks to Hadley Wickham for writing a fantastsic guide to distributing R packages. This package usesformatR::tidy_dir("R") to format code. Apologies about the inconsistent camel_case and snakeCase usaage, I was but a fledgeling programmer.

Introduction

The WGPAN (Whole-Genome Pairwise Alignment Noising) package was designed to deal with neighbor-joining trees built from whole-genome pairwise alignment. Traditional bootstrapping methods are invalid, because there is not a single alignment of all genomes to sample with replacement from. As such, a new method for assigning confidence to nodes in a tree was required. WGPAN allows you to assign confidence values to nodes that are relevant for within clade confidence only. You can therefore test hypotheses regarding user-defined clades, not the relationship among those clades.

In addition, I've included some general utilities to make life a little easier when manipulating trees with the excellent package APE. The vignette and documentation is forthcoming for these methods.

Installation

Using github

library(devtools)
install_github("bradfordcondon/WGPAN")

This package is only available via github. If you are interested in maintaining this package i would happily hand over control.

Vignettes

For example usage of the bootstrapping methods, please see the vignette