Partial Order Alignment for multiple sequence alignment
POA is Partial Order Alignment, a fast program for multiple sequence
alignment (MSA) in bioinformatics. Its advantages are speed,
scalability, sensitivity, and the superior ability to handle branching
/ indels in the alignment. Partial order alignment is an approach to
MSA, which can be combined with existing methods such as progressive
alignment. POA optimally aligns a pair of MSAs and which therefore can
be applied directly to progressive alignment methods such as CLUSTAL.
For large alignments, Progressive POA is 10-30 times faster than
poa for Debian
POA needs a matrix file to operate. The matrices shipped in the sources of POA can
be found in /usr/share/poa/.
You can test POA with the following command:
poa -read_fasta /usr/share/doc/poa/examples/multidom.seq -clustal /dev/stdout -v /usr/share/poa/blosum80.mat
The original POA archive contains a perl script called "make_pscores.pl", which
can be found in /usr
-- POA INSTALLATION NOTES --
September 2001, updated March 2004.
Dept. of Chemistry & Biochemistry
To compile this program, simply type 'make poa'.
This produces an executable for sequence alignment (poa) and also a
linkable library liblpo.a. The software has been compiled and tested
on LINUX and Mac OS X.
II. RUNNING POA
POA has a variety of command line opt
poa (2.0+20060928-1) unstable; urgency=low
The Debian package version 2.0-1 was built on the upstream sources
"poa_release_2_0.tar.gz" which unfortunately contained an earlier 1.x version
of poa. The new Debian package version 2.0+20060928-1 is thus a major
upgrade. In its version 2.0, poa does not support the same file formats as
before. Please refer to the documentation of poa to chec
poa - align a se
poa (2.0+20060928-3) unstable; urgency=low
[ Charles Plessy ]
* Updated my email address.
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