indelcoder-methods: Codes gaps

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

Codes gaps

Description

Function for coding gaps separately. Only simple indel coding method is available in the current version.

Usage

## S4 method for signature 'Dna'
indelcoder(x)

Arguments

x	an object of class Dna.

Value

a list with two components:

indels:

a matrix giving the indel positions (beginnings and ends) and lengths.

codematrix:

a binary matrix giving the indel codings. Missing values are denoted by -1.

Methods

signature(x = "Dna")

Function for coding gaps separately.

Author(s)

Caner Aktas, [e-mail]

References

Simmons, M., Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49, 369-381.

See Also

distance

Examples

data("dna.obj")
x<-dna.obj

## Simple indel coding.
indelcoder(x)

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