Your message dated Sat, 21 Jul 2007 11:54:29 +0900
with message-id <[EMAIL PROTECTED]>
and subject line Using muscle instead of t-coffee.
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--- Begin Message ---
Package: seaview
Version: 20021127-4.1
Severity: wishlist
Dear Brian Furry,
Seaview has the ability to launch an external multiple alignment
software, clustalw [1], on selected sequences. For this function, it
relies on an external script, seaview_align.sh [2]. On the website of
T-coffee [3], an alternative seaview_align.sh file is provided [4] to
launch T-Coffee instead of clustalw.
[1] http://packages.debian.org/unstable/science/clustalw
[2] /usr/bin/seaview_align.sh
[3] http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
[4] http://igs-server.cnrs-mrs.fr/~cnotred/Packages/seaview_align.sh
I think that it would be interesting to provide it to the users of
seaview in Debian for two reasons :
- T-Coffee is thought to be more accurate (and slower) than clustalw.
- T-Coffee is free, clustalw is in non-free.
Now how to implement this? It seems that if we recommand the users to
copy the alternative seaview_align.sh in /usr/bin, the md5 sums will
differ in case of integrity check. Should the /etc/alternatives system
be used for that case?
In the case a licence is needed for the alternative seaview_align.sh
script, I volunteer to contact the author...
Best regards,
--
Charles Plessy
Wako, Saitama, Japan
-- 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 2.6.15sound
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Versions of packages seaview depends on:
ii libc6 2.3.5-8 GNU C Library: Shared libraries an
ii libfltk1.1 1.1.6-10 Fast Light Toolkit shared librarie
ii libgcc1 1:4.0.2-5 GCC support library
ii libstdc++6 4.0.2-5 The GNU Standard C++ Library v3
ii libx11-6 6.9.0.dfsg.1-4 X Window System protocol client li
ii libxext6 6.9.0.dfsg.1-2 X Window System miscellaneous exte
ii libxft2 2.1.7-1 FreeType-based font drawing librar
Versions of packages seaview recommends:
ii clustalw 1.83-1 [Biology] Global multiple nucleoti
ii gnome-terminal [x-termin 2.10.0-3 The GNOME 2 terminal emulator appl
ii konsole [x-terminal-emul 4:3.5.1-1 X terminal emulator for KDE
ii xterm [x-terminal-emulat 6.8.2.dfsg.1-11 X terminal emulator
-- no debconf information
--- End Message ---
--- Begin Message ---
Since Seaview now allows to use muscle instead of clustalw, it is not
very important anymore to modify it to use t-coffee (the goal was to
allow SeaView to be moved from 'main' to 'contrib').
--
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan
--- End Message ---
