vhica-package: Vertical and Horizontal Inheritance Consistence Analysis

Description Details Author(s) References Examples

Description

The package implements the VHICA method described in Wallau et al. (in prep). 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. Two files should be provided, for both a set of reference genes and transposable element sequences: (i) pairwise divergence across species (e.g., dS), (ii) codon usage bias for all genes and elements in all species.

Details

Package: vhica
Type: Package
License: GPL-v2

This package contains three main functions.

In addition, it provides tools to calculate divergence (div) and codon usage bias (CUB), which are necessary to apply the VHICA method.

Author(s)

Implementation: Arnaud Le Rouzic <lerouzic@egce.cnrs-gif.fr>
Scientists who designed the method: Gabriel Wallau, Aurélie Hua-Van, Arnaud Le~Rouzic.

Maintainer: Arnaud Le Rouzic <lerouzic@egce.cnrs-gif.fr>

References

Gabriel Luz Wallau, Arnaud Le Rouzic, Pierre Capy, Elgion Loreto, Aurélie Hua-Van. VHICA: A new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila. Molecular biology and evolution 33 (4), 1094-1109.

Examples

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file.cb <- system.file("extdata", "mini-cbias.txt", package="vhica")
file.div <- system.file("extdata", "mini-div.txt", package="vhica")
file.tree <- if(require("ape")) system.file("extdata", "phylo.nwk", package="vhica") else NULL
vc <- read.vhica(cb.filename=file.cb, div.filename=file.div)
plot(vc, "dere", "dana")
im <- image(vc, "mellifera:6", treefile=file.tree, skip.void=TRUE)
summary(im)

vhica documentation built on March 2, 2020, 5:07 p.m.