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: 0.2.1
Depends: R (≥ 3.4.0)
Imports: ape (≥ 5.0), colorspace, gmp, memoise, phangorn (≥ 2.2.1), R.cache, Rcpp, Rdpack, stats
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, shiny, testthat, xlsx
Published: 2018-12-07
Author: Martin R. Smith ORCID iD [aut, cre, cph], Emmanuel Paradis ORCID iD [cph], Klaus Schliep ORCID iD [cph], Martin Brazeau ORCID iD [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: README NEWS
CRAN checks: TreeSearch results

Downloads:

Reference manual: TreeSearch.pdf
Vignettes: Getting started
Inapplicable data
Inapplicable data
Profile parsimony
Profile parsimony
Package source: TreeSearch_0.2.1.tar.gz
Windows binaries: r-devel: TreeSearch_0.2.1.zip, r-release: TreeSearch_0.2.1.zip, r-oldrel: TreeSearch_0.2.1.zip
OS X binaries: r-release: TreeSearch_0.2.1.tgz, r-oldrel: TreeSearch_0.2.1.tgz
Old sources: TreeSearch archive

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