Vertical and Horizontal Inheritance Consistence Analysis
Computes the Codon Usage Bias of DNA sequences
Computation of the synonymous divergence between sequences
Consistency matrix for a transposable element in the VHICA analysis.
Plots a VHICA regression between two species.
Reads divergence and codon usage data files for the VHICA method.
Provides a data.frame that nicely displays the information returned by...
Vertical and Horizontal Inheritance Consistence Analysis
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.