div {vhica}

Computation of the synonymous divergence between sequences

Description

The divergence between DNA sequences can be synonymous (neutral) or non-synonymous. Synonymous differences are generally considered as a better proxy for evolutionary divergence, as it is not affected by selection. This function computes the synonymous divergence between sequences.

Usage

div(file = NULL, sequence = NULL, sqs = NULL, method = "LWL85", 
	pairwise = TRUE, max.lim = 3)

Arguments

file

FASTA file in which aligned sequences are stored.

sequence

Alternatively, the result of seqinr::read.fasta.

sqs

Vector of sequence names to be compared. If not provided, all pairwise comparisons will be performed.

method

Method used to compute the divergence. So far, only the LWL85 method (from Li et al. 1985).

pairwise

Boolean: should the divergence be calculated for each pair of sequences or on the whole dataset? This is of particular importance when indels (gaps) are present in sequences, as codons with gaps are generally discarded by most methods. Setting this option to TRUE is thus more likely to give accurate results with multiple-gap sequences, but the calculation will also be slower.

max.lim

Maximum value for divergence. Depending on the algorithm, various corrections can bring the divergence value above 100%. Values larger than max.lim will be replaced by NAs, as they can be problematic for further statistical tests.

Details

The LWL85 method is a wrapper around the kaks function from the seqinr package.

Value

A 3-column data frame with the following fields:

• div: The divergence score

• sq1: The first sequence in the comparison

• sq2: The second sequence in the comparison

Author(s)

Aurelie Hua-Van and Arnaud Le Rouzic

References

Li, W. H., Wu, C. I., & Luo, C. C. (1985). A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular biology and evolution, 2(2), 150-174.

See Also

CUB

Examples

	seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
	div(seq.file)