Last Change: 2018-09-07, 16:50
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seaview - a multiple sequence alignment editor
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seaview [filename] |
seaview is the program that starts the SeaView GUI.
SeaView is a graphical multiple sequence alignment editor. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS). It allows one to manually edit the alignment, and also to run DOT−PLOT, CLUSTAL or MUSCLE programs to locally improve the alignment.
If started from the command line with filename as an argument, seaview will open the alignment stored in filename.
−fast
Suppresses double buffering for display. This should only accelerate display on very slow systems.
−fontsize n
Sets the font size to n.
−inverted
Residues will appear as black letters on a colored background
−save format_name
Sets the default file format for saving operations. format_name can be either mase, clustal, phylip, msf, fasta, or nexus. Without this option, SeaView autodetects the format of the opened file and uses the same for saving.
$HOME/.seaviewrc holds the user´s configuration for SeaView.
The program is fully documented online. Press the "help" button in the main window. On Debian systems, the text template for SeaView´s help can be found in /usr/share/seaview/seaview.help (It is human readable).
Two multiple alignment programs can be called from whithin SeaView: muscle(1) and clustalw(1).
The home page of SeaView is http://pbil.univ−lyon1.fr/software/seaview.html.
If you use SeaView in a published work, please cite the following reference: Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci., 12, 543−548.
Manolo Gouy <mgouy@biomserv.univ−lyon1.fr>
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Upstream author of SeaView. |
Stéphane Bortzmeyer <bortzmeyer@debian.org>
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Wrote this manpage in DocBook XML for the Debian distribution. |
Charles Plessy <charles−debian−nospam@plessy.org>
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Updated this manpage in DocBook XML for the Debian distribution. |
Copyright © 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007 Manolo Gouy
Copyright © 1999 Stéphane Bortzmeyer
Copyright © 2006, 2007 Charles Plessy
SeaView is released under the GNU General Public Licence
You can redistribute and/or modify this manpage under same terms as SeaView itself.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common−licenses/GPL.