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object --+ | Application.AbstractCommandline --+ | PrankCommandline
Command line wrapper for the multiple alignment program PRANK.
http://www.ebi.ac.uk/goldman-srv/prank/prank/
Example:
To align a FASTA file (unaligned.fasta) with the output in aligned FASTA format with the output filename starting with "aligned" (you can't pick the filename explicitly), no tree ouput and no XML output, use:
>>> from Bio.Align.Applications import PrankCommandline >>> prank_cline = PrankCommandline(d="unaligned.fasta", ... o="aligned", #prefix only! ... f=8, #FASTA output ... notree=True, noxml=True) >>> print prank_cline prank -d=unaligned.fasta -o=aligned -f=8 -noxml -notree
You would typically run the command line with prank_cline() or via the Python subprocess module, as described in the Biopython tutorial.
Citations:
Loytynoja, A. and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences, 102: 10557--10562.
Loytynoja, A. and Goldman, N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320: 1632.
Last checked agains version: 081202
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Create a new instance of a command line wrapper object.
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