prank: PRANK
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy
Description
Usage
Arguments
Value
Note
Author(s)
References
See Also
Description
DNA sequence Alignment Using the program PRANK.
Usage
1
2
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.
Author(s)
Christoph Heibl
References
http://www.ebi.ac.uk/goldman-srv/prank/prank/
See Also
read.fas to import DNA sequences;
mafft for another alignment algorithm;
gblocks and aliscore for alignment cleaning.
fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.
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Description Usage Arguments Value Note Author(s) References See Also
Description
DNA sequence Alignment Using the program PRANK.
Usage
1 2 |
Arguments
x |
an object of class |
outfile |
a character string giving a name for the output file. |
guidetree |
an object of class |
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.
Author(s)
Christoph Heibl
References
http://www.ebi.ac.uk/goldman-srv/prank/prank/
See Also
read.fas to import DNA sequences;
mafft for another alignment algorithm;
gblocks and aliscore for alignment cleaning.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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