aliscore: Masking of Sequence Alignments with ALISCORE

In ips: Interfaces to Phylogenetic Software in R

Masking of Sequence Alignments with ALISCORE

Description

Provides a interface to Aliscore, in order to remove problematic regions of a DNA sequence alignment.

Usage

aliscore(x, gaps = "5state", w = 6, r, t, l, s, o, exec)

Arguments

x	DNA sequences of class DNAbin.
gaps	A vector of mode "character" indicating how gaps shall be treated: as "5state" or as "ambiguous".
w	An integer giving the size of the sliding window.
r	An integer giving the number of random pairwise sequence comparisons; defaults to 4 * N.
t	Not yet implemented.
l	Not yet implemented.
s	Not yet implemented.
o	A vector of mode "character" containing outgroup taxon names.
exec	A character string, giving the path to the Aliscore script.

Value

A matrix of class "DNAbin".

Note

This function was developed with ALISCORE version 2. ALISCORE is no longer available and seems to be discontinued by the authors.

References

Misof, B. and K. Misof. 2009. A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst. Biol. 58: 21–34.

Kueck, P., K. Meusemann, J. Dambach, B. Thormann, B.M. von Reumont, J.W. Waegele and B. Misof. 2010. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Frontiers in Zoology 7: 10.

See Also

mafft and prank for multiple sequence alignment; gblocks for another alignment masking algorithm.

Examples

data(ips.28S)
## Not run: aliscore(ips.28S)

ips documentation built on July 8, 2026, 5:07 p.m.