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amap-align

Protein multiple alignment by sequence annealing

Variants:
AMAP is a command line tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation.

The java visualisation tool of AMAP 2.2 is not yet packaged in Debian.

Homepage:-
Package version:2.2-3
Architecture:ia64
Distribution:Debian
Filename:amap-align_2.2-3_ia64.deb

/usr/share/doc/amap-align/README

See http://baboon.math.berkeley.edu/amap/ for more information.

INSTALL
=======

To build the AMAP alignment code change to the 'align' directory and type:

	% make


This distribution includes the compiled AmapDisplay.jar file. 
In case you want to build the AmapDisplay from the source code, 
you'll need ant (http://ant.apache.org) installed.  
Once ant is installed change to the 'display' dire
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/usr/share/doc/amap-align/README.Debian

amap for Debian
===============

Please note that the previous upstream homepage
  http://bio.math.berkeley.edu/amap/
vanished and there is no information left about further updates
of this program.

The version hosted at
    http://code.google.com/p/amap-align/
is older than the Debian packaged version.

If you have any knowledge about new location of the code, please
drop a note to the address b
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/usr/share/doc/amap-align/NEWS.Debian.gz

amap-align (2.0-2) unstable; urgency=low

  * Previous versions of the package amap-align were shipping the program
    under a binary name (amap-align) which differed from the original one
    (amap) because there was already an amap program in Debian. Since this
    program has been removed from the Etch distribution, amap-align now
    provides its function through the program /usr/bin/align. T
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/usr/share/man/man1/amap.1.gz

AMAP(1)                      User Manual                     AMAP(1)



NAME
       amap - Protein m
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/usr/share/doc/amap-align/changelog.Debian.gz

amap-align (2.2-3) unstable; urgency=low

  * Standards-Version: 3.9.2 (no changes needed)
  * Debhe
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/usr/share/doc/amap-align/copyright

X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
X-Debianized-By: Charles Pl
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