homopoly-methods: Provides the list of homoplastic indels and substitutions

In haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Provides the list of homoplastic indels and substitutions

Description

This function returs the list of homoplastic indels and substitutions.

Usage

## S4 method for signature 'Dna'
homopoly(x,indels="sic",...)

Arguments

x	an object of class Dna.
indels	the indel coding method to be used. This must be one of "sic", "5th" or "missing". Any unambiguous substring can be given. See distance for details.
...	additional arguments to parsimnet.

Value

a list with following components:

indels	a character vector of homoplastic indels sitewise Consistency Index, names of the character vector gives the site of homoplastic indel.
subs	a character vector of homoplastic substitutions sitewise Consistency Index, names of the character vector gives the site of substitution.

Methods

signature(x = "Dna")

Author(s)

Caner Aktas, [e-mail]

Examples

data("dna.obj")

### Method for signature 'Dna'.
x<-dna.obj
homopoly(x)

haplotypes documentation built on July 26, 2023, 5:22 p.m.