deleteGaps: Remove Gap Positions From DNA Sequences

In ips: Interfaces to Phylogenetic Software in R

Remove Gap Positions From DNA Sequences

Description

Remove indel positions (or gaps) from a DNA sequence alignment. For faster execution, deleteGaps handles sequences in ape's bit-level coding scheme.

Usage

deleteGaps(x, gap.max = nrow(x) - 4)

Arguments

x	An object of class DNAbin.
gap.max	An integer, which gives the maximum number of gap characters ("-") that will be tolerated at any given alignment position (column). Only values between 0 and nrow(x) - 4 make sense phylogenetically.

Details

The default, nmax = nrow(x) - 4, removes all those positions from the alignment, which contain at least four non-gap characters, which is the minimum number of sequences needed to produce a non-trivial unrooted topology. All gaps will be excluded by selecting nmax = 0 and half of all gaps with nmax = nrow(x) / 2.

In contrast, del.gaps removes all gap characters from the alignment, so most probably the result will not be a set of sequences of equal length and the matrix will be coerced to a list.

Value

An object of class DNAbin.

See Also

code.simple.gaps for coding of simple gaps, del.gaps for removal of all gap symbols from an alignment, gblocks and aliscore for more sophisticated methods of cleaning/masking alignments.

ips documentation built on May 29, 2024, 4:39 a.m.