aliscore

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

Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.

Martin R. Smith

Interfaces to Phylogenetic Software in R

Christoph Heibl

Natalie Cusimano

Franz-Sebastian Krah

aliscore function

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

Arguments

Masking of Sequence Alignments with ALISCORE — aliscore

<dl>

<dt>x</dt>
<dd>DNA sequences of class <code>DNAbin</code>.</dd>


<dt>gaps</dt>
<dd>A vector of mode <code>"character"</code> indicating how gaps shall be
treated: as <code>"5state"</code> or as <code>"ambiguous"</code>.</dd>


<dt>w</dt>
<dd>An integer giving the size of the sliding window.</dd>


<dt>r</dt>
<dd>An integer giving the number of random pairwise sequence
comparisons; defaults to <code>4 * N</code>.</dd>


<dt>t</dt>
<dd>Not yet implemented.</dd>


<dt>l</dt>
<dd>Not yet implemented.</dd>


<dt>s</dt>
<dd>Not yet implemented.</dd>


<dt>o</dt>
<dd>A vector of mode <code>"character"</code> containing outgroup taxon names.</dd>


<dt>exec</dt>
<dd>A character string, giving the path to the Aliscore script.</dd>

</dl>

aliscore: Masking of Sequence Alignments with ALISCORE

Description

Usage

Value

Arguments

References

See Also

Examples