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: 0.3.0
Depends: R (≥ 3.4.0)
Imports: ape (≥ 5.0), clue, colorspace, memoise, phangorn (≥ 2.2.1), R.cache, Rdpack, stats
LinkingTo: Rcpp
Suggests: knitr, Rcpp, rmarkdown, shiny, testthat, xlsx
Published: 2019-03-21
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: NEWS
CRAN checks: TreeSearch results

Downloads:

Reference manual: TreeSearch.pdf
Vignettes: Getting started: installation and setup
Tree search with inapplicable data
Load phylogenetic data
Calculating concavity profiles for profile parsimony
Tree search with profile parsimony
Package source: TreeSearch_0.3.0.tar.gz
Windows binaries: r-devel: TreeSearch_0.3.0.zip, r-release: TreeSearch_0.3.0.zip, r-oldrel: TreeSearch_0.3.0.zip
OS X binaries: r-release: TreeSearch_0.3.0.tgz, r-oldrel: TreeSearch_0.3.0.tgz
Old sources: TreeSearch archive

Reverse dependencies:

Reverse imports: Quartet
Reverse suggests: CongreveLamsdell2016

Linking:

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