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
