All code is Copyright (c) 2002-2015 University of
California, Cornell University.
RPHAST is an R interface to the PHAST software
(Phylogenetic Analysis with Space/Time Models).  It can be used for
many types of analysis in comparative and evolutionary genomics,
such as estimating models of evolution from sequence data, scoring
alignments for conservation or acceleration, and predicting
elements based on conservation or custom phylogenetic hidden Markov
models.  It can also perform many basic operations on multiple
sequence alignments and phylogenetic trees.

Get 'Silhouettes' of 'Organisms' from 'Phylopic'
Work with 'Phylopic' web service (<http://phylopic.org/api/>)
to get 'silhouette' images of 'organisms', search names, and more.
Includes functions for adding 'silhouettes' to both base plots and
ggplot2 plots.
c(
person("Scott", "Chamberlain", role = c("aut", "cre"),
email = "myrmecocystus@gmail.com",
comment = c(ORCID = "0000-0003-1444-9135")),
person("David", "Miller", role = "ctb",
email = "dave@ninepointeightone.net")
)
ggplot2, crul (>= 0.5.2), jsonlite, grid, gridBase, graphics,
png
Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
David Miller [ctb]

testthat, vcr (>= 0.2.0), knitr, rmarkdown, R.rsp

c(
person("Brian", "O'Meara", email = "omeara.brian@gmail.com", role = c("aut", "cre")),
person("Abu Saleh", "Md Tayeen", email = "abusalehmdtayeen@gmail.com", role = "aut"))
This wraps the 'Phylotastic' services APIs <https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.
httr, jsonlite, ape, utils, phylobase, methods, rentrez (>=
1.0.4)
Brian O'Meara [aut, cre],
Abu Saleh Md Tayeen [aut]

c(
person("Dirk", "Schumacher", email = "mail@dirk-schumacher.net", role = c("aut", "cre")),
person("Armin", "Biere", role = c("ctb", "cph"), comment = "Author and copyright holder of included PicoSAT code"))
Bindings for the 'PicoSAT' solver to solve Boolean satisfiability problems (SAT).
The boolean satisfiability problem asks the question if a given boolean formula can be TRUE;
i.e. does there exist an assignment of TRUE/FALSE for each variable such that the whole formula is TRUE?
The package bundles 'PicoSAT' solver release 965 <http://www.fmv.jku.at/picosat/>.
Dirk Schumacher [aut, cre],
Armin Biere [ctb, cph] (Author and copyright holder of included PicoSAT
code)