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Bug#378290: marked as done (RFP: proalign -- Probabilistic multiple alignment program)

Your message dated Tue, 25 May 2010 13:22:45 +0900
with message-id <20100525042245.GB6611@kunpuu.plessy.org>
and subject line No plan to package proalign anymore.
has caused the Debian Bug report #378290,
regarding RFP: proalign -- Probabilistic multiple alignment program
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
378290: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=378290
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>

  Package name    : proalign
  Version         : 0.5alpha1
  Upstream Author : Ari Löytynoja & Michel C. Milinkovitch
  URL             : http://evol-linux1.ulb.ac.be/ueg/ProAlign/
  License         : (GPL, LGPL, BSD, MIT/X, etc.)
  Description     : Probabilistic multiple alignment program

 ProAlign performs probabilistic sequence alignments using hidden Markov
 models (HMM). It includes a graphical interface (GUI) allowing to (i)
 perform alignments of nucleotide or amino-acid sequences, (ii) view the
 quality of solutions, (iii) filter the unreliable alignment regions and
 (iv) export alignments to other softwares.
 .
 ProAlign uses a progressive method, such that multiple alignment is
 created stepwise by performing pairwise alignments in the nodes of a
 guide tree. Sequences are described with vectors of character
 probabilities, and each pairwise alignment reconstructs the ancestral
 (parent) sequence by computing the probabilities of different
 characters according to an evolutionary model. It has been published in
 Bioinformatics. 2003 Aug 12;19(12):1505-13.
 .
  Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/


-- System Information:
Debian Release: testing/unstable
  APT prefers unstable
  APT policy: (500, 'unstable'), (500, 'testing')
Architecture: powerpc (ppc64)
Shell:  /bin/sh linked to /bin/bash
Kernel: Linux 2.6.16farm
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)

--- End Message ---
--- Begin Message --- 
I originally planned to package Proalign in my effort of bringing a large
number of multiple sequence alignment programs in Debian. I think that I have
reached that goal (see http://wiki.debian.org/SequenceAlignment), even
in the absence of Proalign.

For the moment, I will focus my efforts in other areas (in particular
next-generation sequencing). But please feel free to request the packaging of
Proalign if you need it.

-- 
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan

--- End Message ---
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