apex: Phylogenetic Methods for Multiple Gene Data
Version 1.0.2

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.

Browse man pages Browse package API and functions Browse package files

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
URL https://github.com/thibautjombart/apex
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("apex")

Man pages

accessors: multidna Accessors
add.gaps: Add gap-only sequences for missing data
apex: apex: Extensions of Ape for Multiple Gene Data
concatenate: Concatenate genes into a single matrix
dist.multidna: Pairwise distances for multiple gene data
getTree: Build phylogenies from multiple gene data
initialize-multidna-method: multidna constructor
initialize-multiphyDat-method: multiphyDat constructor
multidna: multidna: class for multiple gene data
multidna2alignment: Convert from multidna into alignment (seqinr)
multidna2genind: Convert multidna into genind
multidna2multiphyDat: Conversions between multidna and multiphyDat
multiphyDat: multiphyDat: class for multiple gene data
plot-multidna-ANY-method: Display multidna objects
readfiles: Read multiple DNA alignments
rm.gaps: Remove gap-only sequences for missing data
show-multidna-method: Display multidna objects
show-multiphyDat-method: Display multiphyDat objects
subset.multidna: Subset multidna objects

Functions

[,multidna,ANY,ANY,ANY-method Man page
[,multidna-method Man page
[,multiphyDat,ANY,ANY,ANY-method Man page
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
checkIDs Source code
checkLocusNames Source code
concatenate Man page
concatenate,multidna-method Man page
concatenate,multiphyDat-method Man page
dist.multidna Man page Source code
find_gap_sequence Source code
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 Source code
initialize,multidna-method Man page
initialize,multidna-methods Man page
initialize,multiphyDat-method Man page
initialize,multiphyDat-methods Man page
multidna Man page
multidna-class Man page
multidna2alignment Man page Source code
multidna2genind Man page Source code
multidna2multiphyDat Man page Source code
multiphyDat Man page
multiphyDat-class Man page
multiphyDat2alignment Man page Source code
multiphyDat2genind Man page Source code
multiphyDat2multidna Man page Source code
nMissingSequences Source code
new.multidna Man page
new.multiphyDat Man page
plot,multidna,ANY-method Man page
plot,multidna-method Man page
read.multiFASTA Man page Source code
read.multidna Man page Source code
read.multiphyDat Man page Source code
rm.gaps Man page
rm.gaps,multidna-method Man page
rm.gaps,multiphyDat-method Man page
sGapOnly Source code
sGapOnlyPhyDat Source code
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

inst
inst/patr_poat49.fasta
inst/patr_poat43.fasta
inst/patr_poat48.fasta
inst/doc
inst/doc/apex.R
inst/doc/apex.Rmd
inst/doc/apex.html
inst/patr_poat47.fasta
tests
tests/testthat.R
tests/testthat
tests/testthat/test_export.R
NAMESPACE
R
R/readfiles.R
R/multiphyDat.class.R
R/getTree.R
R/rm.gaps.R
R/subset.R
R/accessors.R
R/multidna.constructor.R
R/plot.R
R/exports.R
R/show.R
R/multiphyDat.constructor.R
R/multidna.class.R
R/internal.R
R/doc.R
R/dist.R
R/concatenate.R
R/add.gaps.R
R/datasets.R
vignettes
vignettes/apex.Rmd
vignettes/figs
vignettes/figs/class-1.png
vignettes/figs/class-2.png
vignettes/figs/concat-2.png
vignettes/figs/plotMultiPhylo-1.png
vignettes/figs/handling-1.png
vignettes/figs/plotPhyloSingle-1.png
vignettes/figs/handling-2.png
vignettes/figs/multidnaclass-1.png
vignettes/figs/multidnaclass-2.png
vignettes/figs/readfiles-1.png
vignettes/figs/concat-1.png
vignettes/figs/plotPmlPart-1.png
vignettes/apex.md
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/show-multidna-method.Rd
man/readfiles.Rd
man/initialize-multidna-method.Rd
man/subset.multidna.Rd
man/multidna2multiphyDat.Rd
man/add.gaps.Rd
man/getTree.Rd
man/rm.gaps.Rd
man/multiphyDat.Rd
man/initialize-multiphyDat-method.Rd
man/plot-multidna-ANY-method.Rd
man/multidna2genind.Rd
man/multidna.Rd
man/show-multiphyDat-method.Rd
man/dist.multidna.Rd
man/accessors.Rd
man/apex.Rd
man/concatenate.Rd
man/multidna2alignment.Rd
apex documentation built on May 19, 2017, 7:35 a.m.