prank {ips}

PRANK

Description

DNA sequence Alignment Using the program PRANK.

Usage

prank(x, outfile, guidetree = NULL, gaprate = 0.025, 
    gapext = 0.75, path)

Arguments

x

an object of class DNAbin.

outfile

a character string giving a name for the output file.

guidetree

an object of class phylo to be used as guidetree in alignment.

gaprate

numeric giving the gap opening rate; defaults to 0.025.

gapext

numeric giving the gap extension penalty; defaults to 0.75.

path

a character string indicating the path to the PRANK executable.

Value

matrix of class "DNAbin"

Note

prank was last updated and tested to work with PRANK v. 120814 on Windows XP. If you have problems getting the function to work with a newer version of PRANK, contact the package maintainer.

References

http://wasabiapp.org/software/prank/

See Also

read.fas to import DNA sequences; mafft for another alignment algorithm; gblocks and aliscore for alignment cleaning.