TreeSearch: Phylogenetic Tree Search Using Custom Optimality Criteria

Searches for phylogenetic trees that are optimal using a user-defined criterion. Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) <doi:10.2307/2412182>. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>.

Version:	0.2.2
Depends:	R (≥ 3.4.0)
Imports:	ape (≥ 5.0), colorspace, gmp, memoise, phangorn (≥ 2.2.1), R.cache, Rdpack, stats
LinkingTo:	Rcpp
Suggests:	knitr, Rcpp, rmarkdown, shiny, testthat, xlsx
Published:	2019-01-02
Author:	Martin R. Smith [aut, cre, cph], Emmanuel Paradis [cph], Klaus Schliep [cph], Martin Brazeau [cph]
Maintainer:	Martin R. Smith <martin.smith at durham.ac.uk>
BugReports:	https://github.com/ms609/TreeSearch/issues
License:	GPL (≥ 3)
Copyright:	Incorporates C/C++ code from: ape by Emmanuel Paradis; phangorn by Klaus Scheip <doi:10.1093/bioinformatics/btq706>; Morphy Phylogenetic Library by Martin Brazeau <https://github.com/mbrazeau/MorphyLib> (GPL3)
URL:	https://github.com/ms609/TreeSearch
NeedsCompilation:	yes
Language:	en-GB
Citation:	TreeSearch citation info
Materials:	NEWS
CRAN checks:	TreeSearch results

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