Remove indel positions (or gaps) from a DNA sequence
alignment. For faster execution, deleteGaps handles sequences
in ape's bit-level coding scheme.
deleteGaps(x, gap.max = nrow(x) - 4)An object of class DNAbin.
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.
An object of class DNAbin.
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.
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.