ape (version 3.3)

del.gaps: Delete Alignment Gaps in DNA Sequences

Description

These functions remove indel gaps ("-") in a sample of DNA sequences.

Usage

del.gaps(x)
del.colgapsonly(x)

Arguments

x
a matrix, a list, or a vector containing the DNA sequences; only matrices for del.colgapsonly.

Value

  • del.gaps returns a vector (if there is only one input sequence) or a list of class "DNAbin"; del.colgapsonly returns a matrix.

Details

del.gaps remove all gaps, so the returned sequences may not have all the same lengths and are therefore returned in a list.

del.colgapsonly removes the columns that contain only gaps (useful when a small matrix is extracted from a large alignment).

The sequences can be either in "DNAbin" or in another format, but the returned object is always of class "DNAbin".

See Also

base.freq, GC.content, seg.sites, image.DNAbin