This repository comprises various scripts for preparing, processing and manipulating phylogenetic trees and associated data. These are summarised here, see the documentation of each script using the help argument.
phylabel.R relabels the tips and/or nodes of a phylogenetic tree according to other supplied data, such as taxonomy and metadata
treedentify.R infers taxonomic classification for unknown terminals on a tree based on node taxonomisation performed by phylabel.R
partitioner.py expands basic partition tables as output by catfasta2phyml.pl into gene, codon and/or direction-based partitions in RAxML or nexus formats
droptips.R drops tips from a phylogeny
phynames.R reports the tip labels of a phylogenetic tree
grafttree.R grafts one phylogeny to a specified node in a host phylogeny with Open Tree of Life node IDs
constraintbuilder.R builds a constraint phylogeny from a template phylogeny of taxonomic levels
and a taxonomy table. Nested taxonomic levels can be used within the template, e.g.
(Mammalia, Metazoa), which will resolve into
((mammal1, mammal2), (nonmammalmetazoa1, nonmammalmetazoa2)) to easily set one sub-taxon to be
sister to all other sub taxa in a given clade.
taxonomicindices.R computes the taxonomic retention and consistency indices for a given phylogeny and taxonomy table
unresolver.R unresolves nodes in a phylogeny according to a support threshold
phylofuncs.R provides a variety of R functions for working with phylogenetic trees in R
All of the above scripts apart from phylofuncs.R are designed for CLI usage.
Download the specific script you need or git clone the repository. The R scripts require an up to date installation of R.
The CLI R scripts are designed for Linux although will probably work on Mac. They are untested on Windows. They require the R libraries ape, getopt, geiger, taxize and plyr, you can install these easily by running:
Rscript -e 'x<-c("ape", "getopt", "geiger", "taxize", "plyr");install.packages(x[!x %in% installed.packages()[,"Package"]], repos = "https://cloud.r-project.org")'
phylofuncs.R may require other libraries.
The install.sh and uninstall.sh scripts provided can be used to automatically install the necessary R libraries and make the R scripts available on the PATH. This is very much a barebones method and may not work on many operating systems and configurations - it is only tested on Ubuntu Linux.
Clone the repository to a sensible location, e.g. ~/software/ for a local installation or /opt/ for installation for all users.
git clone https://github.com/tjcreedy/phylostuff.git
Run the installation script. Running as sudo will attempt to create symlinks in /usr/local/bin/, otherwise the script will add a line to your .bashrc file to add the directory to your PATH.
cd phylostuff
bash install.sh
# or
sudo bash install.sh
To unistall, you must be in the phylostuff directory
bash uninstall.sh
# or
sudo bash uninstall.sh