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Last data update: 2014.03.03

R: Masking of Sequence Alignments with ALISCORE

aliscore

R Documentation

Masking of Sequence Alignments with ALISCORE

Description

This function provides a wrapper to Aliscore, which can be used remove problematic regions of a sequence alignment.

Usage

aliscore(x, gaps = "5state", w = 6, r, t, l, s, o, 
        path = "/Applications/Aliscore_v.2.0")

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.
`path`	A character string, giving the path to the Aliscore script.

Value

matrix of class "DNAbin"

Note

This function was developed with ALISCORE version 2.

Author(s)

Christoph Heibl

References

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.