big.phylo

An R package to construct phylogenies for very large numbers of sequences

Installation

This software package requires third party code, please only proceed once installed:

• Open MPI: http://www.open-mpi.org/

The easiest way to install big.phylo is via the devtools package:

# install.packages("devtools")
library(devtools)
install_github("olli0601/big.phylo")

Help

Help files and documentation are available once the package is loaded in R with 'require(big.phylo)'. Documentation is available via 'library(help="big.phylo")'. The package contains:

• functions to create ExaML bootstrap phylogenies. Try ?pipeline.ExaML.bootstrap.per.proc

• an Rscript and functions to remove drug resistance mutations. Try ?seq.rm.drugresistance. This function is also accessible from the command line via

Rscript rm.drm.Rscript -indir=XXX -infile=XXY  -outdir=XYY -outfile=YYY

where rm.drm.Rscript is found in the R package installation directory.