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 (2017) <doi:10.1101/209775>.

Version: 0.1.2
Depends: R (≥ 3.4.0)
Imports: ape (≥ 5.0), memoise, phangorn (≥ 2.2.1), R.cache, Rdpack, stats
Suggests: knitr, rmarkdown, shiny, testthat, xlsx
Published: 2018-03-19
Author: Martin R. Smith ORCID iD [aut, cre, cph], Emmanuel Paradis [cph], Martin Brazeau [cph]
Maintainer: Martin R. Smith <martins at gmail.com>
BugReports: https://github.com/ms609/TreeSearch/issues
License: GPL (≥ 3)
Copyright: Incorporates C code from: ape by Emmanuel Paradis; Morphy Phylogenetic Library by Martin Brazeau <https://github.com/mbrazeau/MorphyLib> (GPL3)
URL: https://github.com/ms609/TreeSearch
NeedsCompilation: yes
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_0.1.2.tar.gz
Windows binaries: r-devel: TreeSearch_0.1.2.zip, r-release: TreeSearch_0.1.2.zip, r-oldrel: TreeSearch_0.1.2.zip
OS X binaries: r-release: TreeSearch_0.1.2.tgz, r-oldrel: TreeSearch_0.1.2.tgz
Old sources: TreeSearch archive

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