Imports: Rcpp (>= 0.11.0), adephylo, igraph, ape, phylobase, boot, DBI,
graphics, grDevices, methods, stats, utils

Title: R packge for simulating biological sequence evolution
Author: Botond Sipos <sbotond@ebi.ac.uk>, Gregory Jordan
Description: PhyloSim is an extensible object-oriented framework for
the Monte Carlo simulation of sequence evolution written in 100
percent R. It is built on the top of the R.oo and ape packages
and uses Gillespie's direct method to simulate substitutions,

Title: R package for simulating biological sequence evolution

Author: Botond Sipos <sbotond@ebi.ac.uk>, Gregory Jordan <greg@ebi.ac.uk>
Imports: R.methodsS3, R.oo, ape, compoisson, ggplot2
Description: PhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions.

Title: Flexible Simulations of Biological Sequence Evolution
Author: Botond Sipos <sbotond@gmail.com>, Gregory Jordan <greg@ebi.ac.uk>
Description: An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions.

Description: An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions. Citation: Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment <doi:10.1186/1471-2105-12-104>.

Title: Automated Phylogenetic Sequence Cluster Identification from
Authors@R: c(person("Hannes", "Hettling", role = "aut"), person("Rutger", "Vos", role = "aut"), person("Alexander", "Zizka", role = "aut"), person("Dom", "Bennett", role = c("aut", "cre"), email = "dominic.john.bennett@gmail.com"), person("Alexandre", "Antonelli", role = c("aut")))
Description: A pipeline for the identification, within taxonomic groups, of
'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a
phylogenetic analysis. The pipeline depends on a local alignment search tool
and is, therefore, not dependent on differences in gene naming conventions
Imports: igraph, rentrez, XML, ggplot2, sys, treeman, treemapify,