prank

DNA sequence Alignment Using the program PRANK.

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

prank function

<dl>	
 <dt>x</dt>
<dd>an object of class <code>DNAbin</code>.</dd> 
 <dt>outfile</dt>
<dd>a character string giving a name for the output file.</dd> 
 <dt>guidetree</dt>
<dd>an object of class <code>phylo</code> to be used as guidetree in alignment.</dd> 
 <dt>gaprate</dt>
<dd>numeric giving the gap opening rate; defaults to 0.025.</dd> 
 <dt>gapext</dt>
<dd>numeric giving the gap extension penalty; defaults to 0.75.</dd> 
 <dt>path</dt>
<dd>a character string indicating the path to the PRANK executable.</dd> 
</dl>

Arguments

PRANK — prank

<dl>

	
 <dt>x</dt>
<dd>an object of class <code>DNAbin</code>.</dd>

 
 <dt>outfile</dt>
<dd>a character string giving a name for the output file.</dd>

 
 <dt>guidetree</dt>
<dd>an object of class <code>phylo</code> to be used as guidetree in alignment.</dd>

 
 <dt>gaprate</dt>
<dd>numeric giving the gap opening rate; defaults to 0.025.</dd>

 
 <dt>gapext</dt>
<dd>numeric giving the gap extension penalty; defaults to 0.75.</dd>

 
 <dt>path</dt>
<dd>a character string indicating the path to the PRANK executable.</dd>

 
</dl>

prank: PRANK

Description

Usage

Value

Arguments

References

See Also