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>.

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Description file content

Package
TreeSearch
Title
Phylogenetic Tree Search Using Custom Optimality Criteria
Version
0.2.0
Date
2018-09-06
License
GPL (>= 3)
Copyright
Incorporates C code from: ape by Emmanuel Paradis; 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 (2017) .
URL
BugReports
https://github.com/ms609/TreeSearch/issues
Depends
R (>= 3.4.0)
Imports
ape (>= 5.0), colorspace, gmp, memoise, phangorn (>= 2.2.1), R.cache, Rdpack, stats
Suggests
knitr, rmarkdown, shiny, testthat, xlsx
RdMacros
Rdpack
LazyData
true
ByteCompile
true
Encoding
UTF-8
VignetteBuilder
knitr
RoxygenNote
6.1.0
NeedsCompilation
yes
Packaged
2018-09-10 11:21:54 UTC; ms609
Author
Martin R. Smith [aut, cre, cph] (), Emmanuel Paradis [cph], Martin Brazeau [cph]
Maintainer
Martin R. Smith
Repository
CRAN
Date/Publication
2018-09-11 11:00:02 UTC

install.packages('TreeSearch')

0.2.0

11 days ago

https://github.com/ms609/TreeSearch

Martin R. Smith

GPL (>= 3)

Depends on

R (>= 3.4.0)

Imports

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

Suggests

knitr, rmarkdown, shiny, testthat, xlsx

Discussions