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.

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.

Aliscore website: https://bonn.leibniz-lib.de/en/research/research-centres-and-groups/aliscore

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 May 29, 2024, 4:39 a.m.