deleteGaps: Remove Gap Positions From DNA Sequences
In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

Description Usage Arguments Details Value See Also

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

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

`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.

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.

An object of class DNAbin.

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.

heibl/polenta documentation built on May 17, 2019, 3:22 p.m.