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.

Author
Thibaut Jombart [aut, cre], Zhian Namir Kamvar [aut], Klaus Schliep [aut], Eric Archer [aut], Rebecca Harris [aut]
Date of publication
2016-03-31 17:50:47
Maintainer
Thibaut Jombart <t.jombart@imperial.ac.uk>
License
GPL (>= 2)
Version
1.0.2
URLs

View on CRAN

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

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