Rapid Calculation of Phylogenetic Information Content
c(person("Alex", "Dornburg",email="alex.dornburg@naturalsciences.org",role=c("aut","cre", "cph")),person("J. Nick", "Fisk", email="jnf3769@rit.edu",role=c("aut", "cph")),person("Jules", "Tamagnan",email="jules.tamagnan@yale.edu",role=c("aut", "cph")), person("Jeffrey","Townsend",email="jeffrey.townsend@yale.edu",role=c("aut", "cph")))
Enables rapid calculation of phylogenetic information content using the latest advances in phylogenetic informativeness based theory. These advances include modifications that incorporate uneven branch lengths and any model of nucleotide substitution to provide assessments of the phylogenetic utility of any given dataset or dataset partition. Also provides new tools for data visualization and routines optimized for rapid statistical calculations, including approaches making use of Bayesian posterior distributions and parallel processing. Users can apply these approaches toward screening datasets for phylogenetic/genomic information content.
phytools, splines, gplots, RColorBrewer, foreach, iterators,
geiger, doParallel, gridExtra, hexbin, PBSmodelling, ape,
ggplot2
Alex Dornburg [aut, cre, cph],
J. Nick Fisk [aut, cph],
Jules Tamagnan [aut, cph],
Jeffrey Townsend [aut, cph]

Jason T. Weir <weir@zoology.ubc.ca>, Dolph Schluter <schluter@zoology.ubc.ca>
PhySim contains functions to simulate phylogenetic trees under a virth death model. Functions are provided to model a lag-time to speciation and extract sister species ages.

A Fast, Flexible Tool for Sorting Phylogenetic Trees
c(person("Timothy", "Stephens", email = "timothy.stephens1@uqconnect.edu.au", role = c("aut", "cre", "trl"), comment = "R port"),
person("Debashish", "Bhattacharya", email = "Bhattacharya@AESOP.Rutgers.edu", role = c("aut")),
person("Mark", "Ragan", email = "m.ragan@imb.uq.edu.au", role = c("aut")),
person("Cheong Xin", "Chan", email = "c.chan1@uq.edu.au", role = c("aut", "cph"), comment = "Original Perl implementation"))
Screens and sorts phylogenetic trees in both traditional and
extended Newick format. Allows for the fast and flexible screening (within
a tree) of Exclusive clades that comprise only the target taxa and/or Non-
Exclusive clades that includes a defined portion of non-target taxa.
Timothy Stephens [aut, cre, trl] (R port),
Debashish Bhattacharya [aut],
Mark Ragan [aut],
Cheong Xin Chan [aut, cph] (Original Perl implementation)