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>.

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Description file content

Package
TreeSearch
Title
Phylogenetic Tree Search Using Custom Optimality Criteria
Version
0.3.2
Date
2019-06-03
License
GPL (>= 3)
Copyright
Incorporates C/C++ code from: ape by Emmanuel Paradis; phangorn by Klaus Scheip ; Morphy Phylogenetic Library by Martin Brazeau (GPL3)
Description
Searches for phylogenetic trees that are optimal using a user-defined criterion. Implements Profile Parsimony (Faith and Trueman, 2001) , and Successive Approximations (Farris, 1969) . Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) .
URL
BugReports
https://github.com/ms609/TreeSearch/issues
Depends
R (>= 3.4.0)
Imports
ape (>= 5.0), clue, colorspace, memoise, phangorn (>= 2.2.1), R.cache, Rdpack, stats
Suggests
knitr, Rcpp, rmarkdown, shiny, testthat, xlsx
RdMacros
Rdpack
LazyData
true
ByteCompile
true
LinkingTo
Rcpp
Encoding
UTF-8
Language
en-GB
VignetteBuilder
knitr
RoxygenNote
6.1.1
NeedsCompilation
yes
Packaged
2019-06-03 14:24:19 UTC; ms609
Author
Martin R. Smith [aut, cre, cph] (), Emmanuel Paradis [cph] (), Klaus Schliep [cph] (), Martin Brazeau [cph] ()
Maintainer
Martin R. Smith
Repository
CRAN
Date/Publication
2019-06-03 15:30:03 UTC

install.packages('TreeSearch')

0.3.2

a month ago

https://github.com/ms609/TreeSearch

Martin R. Smith

GPL (>= 3)

Depends on

R (>= 3.4.0)

Imports

ape (>= 5.0), clue, colorspace, memoise, phangorn (>= 2.2.1), R.cache, Rdpack, stats

Suggests

knitr, Rcpp, rmarkdown, shiny, testthat, xlsx

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