HaploDist: HaploDist

In vanderleidebastiani/GenVectors: GenVectors an Integrative Analytical Tool for Phylogeography

Description

Function to extract haplotypes and compute pairwise distances between haplotypes. This function use the functions haplotype of package pagas and dist.dna of package ape.

Usage

HaploDist(x, dist.model = "N", ...)

Arguments

x	A list with the set of DNA sequences (as an object of class "DNAbin" or "haplotype") as used by the function haplotype.
dist.model	A character string used by the function dist.dna to specify the evolutionary model to be used to compute pairwise distances from DNA sequences (default dist.model = "N").
...	Additional arguments to the function dist.dna.

Value

A list with:

call	Arguments used.
haplotypes	A list with haplotypes indices that identify each observation sharing the same haplotype.
individual.per.haplotype	A matrix with individuals per haplotype.
haplotype.distances	A matrix with pairwise distances between haplotypes.

See Also

HaploVectors

Examples

data(segv)
HaploDist(segv$segv.fas)

vanderleidebastiani/GenVectors documentation built on Aug. 9, 2019, 1:41 a.m.