apex: Phylogenetic Methods for Multiple Gene Data

Toolkit for the analysis of multiple gene data. Apex implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.

AuthorThibaut Jombart [aut, cre], Zhian Namir Kamvar [aut], Klaus Schliep [aut], Eric Archer [aut], Rebecca Harris [aut]
Date of publication2016-12-05 18:28:47
MaintainerThibaut Jombart <t.jombart@imperial.ac.uk>
LicenseGPL (>= 2)
Version1.0.2
https://github.com/thibautjombart/apex

View on CRAN

Files in this package

apex
apex/inst
apex/inst/patr_poat49.fasta
apex/inst/patr_poat43.fasta
apex/inst/patr_poat48.fasta
apex/inst/doc
apex/inst/doc/apex.R
apex/inst/doc/apex.Rmd
apex/inst/doc/apex.html
apex/inst/patr_poat47.fasta
apex/tests
apex/tests/testthat.R
apex/tests/testthat
apex/tests/testthat/test_export.R
apex/NAMESPACE
apex/R
apex/R/readfiles.R apex/R/multiphyDat.class.R apex/R/getTree.R apex/R/rm.gaps.R apex/R/subset.R apex/R/accessors.R apex/R/multidna.constructor.R apex/R/plot.R apex/R/exports.R apex/R/show.R apex/R/multiphyDat.constructor.R apex/R/multidna.class.R apex/R/internal.R apex/R/doc.R apex/R/dist.R apex/R/concatenate.R apex/R/add.gaps.R apex/R/datasets.R
apex/vignettes
apex/vignettes/apex.Rmd
apex/vignettes/figs
apex/vignettes/figs/class-1.png
apex/vignettes/figs/class-2.png
apex/vignettes/figs/concat-2.png
apex/vignettes/figs/plotMultiPhylo-1.png
apex/vignettes/figs/handling-1.png
apex/vignettes/figs/plotPhyloSingle-1.png
apex/vignettes/figs/handling-2.png
apex/vignettes/figs/multidnaclass-1.png
apex/vignettes/figs/multidnaclass-2.png
apex/vignettes/figs/readfiles-1.png
apex/vignettes/figs/concat-1.png
apex/vignettes/figs/plotPmlPart-1.png
apex/vignettes/apex.md
apex/README.md
apex/MD5
apex/build
apex/build/vignette.rds
apex/DESCRIPTION
apex/man
apex/man/show-multidna-method.Rd apex/man/readfiles.Rd apex/man/initialize-multidna-method.Rd apex/man/subset.multidna.Rd apex/man/multidna2multiphyDat.Rd apex/man/add.gaps.Rd apex/man/getTree.Rd apex/man/rm.gaps.Rd apex/man/multiphyDat.Rd apex/man/initialize-multiphyDat-method.Rd apex/man/plot-multidna-ANY-method.Rd apex/man/multidna2genind.Rd apex/man/multidna.Rd apex/man/show-multiphyDat-method.Rd apex/man/dist.multidna.Rd apex/man/accessors.Rd apex/man/apex.Rd apex/man/concatenate.Rd apex/man/multidna2alignment.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.