This function removes indel positions (or gaps) from a DNA sequence alignment. For faster execution, deleteGaps handles sequences in ape's bit-level coding scheme.
deleteGaps(x, nmax = nrow(x) - 4)an object of class DNAbin.
an integer number between 0 and nrow(x) - 2, which gives the maximum number of
gap characters ("-") that will be tolerated at any given alignment position (column).
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.