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>.

Total

2,198

Last month

497

Last week

160

Average per day

17

Daily downloads

Total downloads

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

2 months 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