vhica: Vertical and Horizontal Inheritance Consistence Analysis

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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) <DOI:10.1093/molbev/msv341>. 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.

Author
Arnaud Le Rouzic
Date of publication
2016-04-05 10:22:33
Maintainer
Arnaud Le Rouzic <lerouzic@egce.cnrs-gif.fr>
License
GPL-2
Version
0.2.4

View on CRAN

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

Files in this package

vhica
vhica/inst
vhica/inst/extdata
vhica/inst/extdata/mini-div.txt
vhica/inst/extdata/mini-cbias.txt
vhica/inst/extdata/phylo.nwk
vhica/inst/extdata/Genes
vhica/inst/extdata/Genes/Amd.fas
vhica/NAMESPACE
vhica/R
vhica/R/CUB.R
vhica/R/read.vhica.R
vhica/R/plot.vhica.R
vhica/R/div.R
vhica/R/image.vhica.R
vhica/R/vhica-internal.R
vhica/MD5
vhica/DESCRIPTION
vhica/man
vhica/man/div.Rd
vhica/man/plot.vhica.Rd
vhica/man/vhica-package.Rd
vhica/man/image.vhica.Rd
vhica/man/read.vhica.Rd
vhica/man/CUB.Rd