The function reads aligned sequences in a fasta file and estimates the codon usage bias for each sequence. Several methods exist to estimate CUB; so far, only the "Effective Number of Codons" (ENC) calculation is available.

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.

Arnaud Rouzic

vhica

Vertical and Horizontal Inheritance Consistence Analysis

CUB function

<dl> <dt>file</dt>
<dd>FASTA file in which aligned sequences are stored.</dd> <dt>sequence</dt>
<dd>Alternatively, the result of seqinr::read.fasta.</dd> <dt>method</dt>
<dd>The method used to compute CUB. "ENC": Effective Number of Codons, as described in Wright (1990).</dd></dl>

Arguments

Aurelie Hua-Van and Arnaud Le Rouzic.

Author

Computes the Codon Usage Bias of DNA sequences — CUB

<dl>

 <dt>file</dt>
<dd>FASTA file in which aligned sequences are stored.</dd>

 <dt>sequence</dt>
<dd>Alternatively, the result of seqinr::read.fasta.</dd>

 <dt>method</dt>
<dd>The method used to compute CUB. "ENC": Effective Number of Codons, as described in Wright (1990).</dd>

</dl>

CUB: Computes the Codon Usage Bias of DNA sequences

Description

Usage

Value

Arguments

Author

References

See Also

Examples