indelcoder-methods {haplotypes}

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)