spider (version 1.2-0)

checkDNA: Check a DNA alignment for missing data

Description

This functions counts the number of bases in an alignment that are composed of missing data.

Usage

checkDNA(DNAbin, gapsAsMissing = TRUE)

Arguments

DNAbin

A DNA alignment of class `DNAbin'.

gapsAsMissing

Logical. Should gaps (coded as '-') be considered missing bases? Default of TRUE.

Value

• A numeric vector giving the number of missing bases in each sequence of the alignment.

Details

This function considers bases coded as '?' and 'N' as missing data. By default, gaps (coded as '-') are also considered missing.

Examples

data(anoteropsis)
checkDNA(anoteropsis)
checkDNA(anoteropsis, gapsAsMissing=FALSE)