ips (version 0.0.11)

aliscore: 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".

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://www.zfmk.de/en/research/research-centres-and-groups/aliscore

See Also

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

Examples

# NOT RUN {
data(ips.28S)
# }
# NOT RUN {
aliscore(ips.28S)
# }