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poa

Partial Order Alignment for multiple sequence alignment

Variants:
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 CLUSTALW. POA is published in Bioinformatics. 2004 Jul 10;20(10):1546-56.
Homepage:
Package version:2.0+20060928-2
Architecture:amd64
Distribution:Debian
Filename:poa_2.0+20060928-2_amd64.deb

/usr/share/doc/poa/README.Debian

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
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/usr/share/doc/poa/README.gz

-- POA INSTALLATION NOTES --
September 2001, updated March 2004.

Chris Lee
Dept. of Chemistry & Biochemistry
UCLA


I. COMPILATION

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
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/usr/share/doc/poa/NEWS.Debian.gz

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
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/usr/share/man/man1/poa.1.gz

POA(1)                                                        POA(1)



NAME
       poa - align a se
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/usr/share/doc/poa/changelog.Debian.gz

poa (2.0+20060928-2) unstable; urgency=low

  [ Charles Plessy ]
    * debian/control:
      - Add S
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/usr/share/doc/poa/copyright

This package was debianized by Charles Plessy
<charles-debian-nospam@plessy.org> on Sun, 20 Aug 2006
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