vhica: Vertical and Horizontal Inheritance Consistence Analysis
Version 0.2.4

The "Vertical and Horizontal Inheritance Consistence Analysis" method is described in the following publication: "VHICA: a new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila" by G. Wallau. et al. (2016) . The purpose of the method is to detect horizontal transfers of transposable elements, by contrasting the divergence of transposable element sequences with that of regular genes.

Browse man pages Browse package API and functions Browse package files

AuthorArnaud Le Rouzic
Date of publication2016-04-05 10:22:33
MaintainerArnaud Le Rouzic <lerouzic@egce.cnrs-gif.fr>
LicenseGPL-2
Version0.2.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("vhica")

Man pages

CUB: Computes the Codon Usage Bias of DNA sequences
div: Computation of the synonymous divergence between sequences
image.vhica: Consistency matrix for a transposable element in the VHICA...
plot.vhica: Plots a VHICA regression between two species.
read.vhica: Reads divergence and codon usage data files for the VHICA...
vhica-package: Vertical and Horizontal Inheritance Consistence Analysis

Functions

CUB Man page Source code
ENC Source code
WL85 Source code
capwords Source code
check.input.consistency Source code
check.species Source code
checkseq Source code
div Man page Source code
element.present Source code
get.TE.fam Source code
get.TE.fam.longseq Source code
get.TE.sub Source code
image.vhica Man page Source code
make.col.obj Source code
plot.caption Source code
plot.matrix Source code
plot.phylo Source code
plot.regression Source code
plot.vhica Man page Source code
prepare.phylo Source code
read.codon.bias Source code
read.divergence Source code
read.vhica Man page Source code
reference.regression Source code
remove.space Source code
reverse.sub Source code
seq.codon.bias Source code
seq.codon.bias.clean Source code
seq.codon.bias.format Source code
seq.divergence Source code
stat.matrix Source code
tables2list Source code
vhica Man page
vhica-package Man page

Files

inst
inst/extdata
inst/extdata/mini-div.txt
inst/extdata/mini-cbias.txt
inst/extdata/phylo.nwk
inst/extdata/Genes
inst/extdata/Genes/Amd.fas
NAMESPACE
R
R/CUB.R
R/read.vhica.R
R/plot.vhica.R
R/div.R
R/image.vhica.R
R/vhica-internal.R
MD5
DESCRIPTION
man
man/div.Rd
man/plot.vhica.Rd
man/vhica-package.Rd
man/image.vhica.Rd
man/read.vhica.Rd
man/CUB.Rd
vhica documentation built on May 20, 2017, 4:40 a.m.