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

Functions

accessors Man page
add.gaps Man page
add.gaps,multidna-method Man page
add.gaps,multiphyDat-method Man page
apex Man page
apex-package Man page
concatenate Man page
concatenate,multidna-method Man page
concatenate,multiphyDat-method Man page
dist.multidna Man page
getLocusNames Man page
getLocusNames,multidna Man page
getLocusNames,multidna-method Man page
getLocusNames,multiphyDat Man page
getLocusNames,multiphyDat-method Man page
getNumInd Man page
getNumInd,multidna-method Man page
getNumInd,multiphyDat Man page
getNumInd,multiphyDat-method Man page
getNumLoci Man page
getNumLoci,multidna Man page
getNumLoci,multidna-method Man page
getNumLoci,multiphyDat Man page
getNumLoci,multiphyDat-method Man page
getNumSequences Man page
getNumSequences,multidna Man page
getNumSequences,multidna-method Man page
getNumSequences,multiphyDat Man page
getNumSequences,multiphyDat-method Man page
getSequenceNames Man page
getSequenceNames,multidna Man page
getSequenceNames,multidna-method Man page
getSequenceNames,multiphyDat Man page
getSequenceNames,multiphyDat-method Man page
getSequences Man page
getSequences,multidna Man page
getSequences,multidna-method Man page
getSequences,multiphyDat Man page
getSequences,multiphyDat-method Man page
getTree Man page
initialize,multidna-method Man page
initialize,multidna-methods Man page
initialize,multiphyDat-method Man page
initialize,multiphyDat-methods Man page
multidna Man page
multidna2alignment Man page
multidna2genind Man page
multidna2multiphyDat Man page
[,multidna,ANY,ANY,ANY-method Man page
multidna-class Man page
[,multidna-method Man page
multiphyDat Man page
multiphyDat2alignment Man page
multiphyDat2genind Man page
multiphyDat2multidna Man page
[,multiphyDat,ANY,ANY,ANY-method Man page
multiphyDat-class Man page
new.multidna Man page
new.multiphyDat Man page
plot,multidna,ANY-method Man page
plot,multidna-method Man page
read.multidna Man page
read.multiFASTA Man page
read.multiphyDat Man page
rm.gaps Man page
rm.gaps,multidna-method Man page
rm.gaps,multiphyDat-method Man page
setLocusNames<- Man page
setLocusNames<-,multidna Man page
setLocusNames<-,multidna-method Man page
setLocusNames<-,multiphyDat Man page
setLocusNames<-,multiphyDat-method Man page
show,multidna-method Man page
show,multiphyDat-method Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

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