This function provides a wrapper to Aliscore, which can be used remove problematic regions of a sequence alignment.
aliscore(x, gaps = "5state", w = 6, r, t, l, s, o,
path = "/Applications/Aliscore_v.2.0")DNA sequences of class DNAbin.
A vector of mode "character" indicating how gaps shall be treated: as "5state" or as "ambiguous".
An integer giving the size of the sliding window.
An integer giving the number of random pairwise sequence comparisons; defaults to 4*N.
Not yet implemented.
Not yet implemented.
Not yet implemented.
A vector of mode "character" containing outgroup taxon names.
A character string, giving the path to the Aliscore script.
matrix of class "DNAbin"
http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/Download/index.en.html
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.
mafft and prank for sequence alignment; gblocks for another alignment masking algorithm.