delete.gaps: Remove Indel Positions from an Alignment
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description Usage Arguments Details Value Author(s) See Also

This function removes indel positions (gaps) from a sequence alignment.

1	delete.gaps(x)

`x`	an object of class `DNAbin`.

delete.gaps removes every column (position) that contains the gap character ("-") for at least one sequence in the alignment. The ouput is always an alignment of sequences of equal length. In contrast, del.gaps removes all gap characters from the alignment, so the result will be (most probably) never a set of sequences of equal length.

an object of class DNAbin

Christoph Heibl

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 alignments.

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.