NAME
seaview - a multiplatform, graphical user interface for multiple
sequence alignment and molecular phylogeny.
SYNOPSIS
seaview [filename]
DESCRIPTION
seaview is the program that starts the SeaView GUI.
SeaView is a graphical interface for multiple sequence alignment and
molecular phylogeny. It is able to read various alignment formats (MSF,
CLUSTAL, FASTA, PHYLIP, MASE, NEXUS) and the Newick tree format, and
allows one to manually edit the alignment, to run DOT-PLOT, CLUSTAL or
MUSCLE programs to locally improve the alignment, and also to compute,
draw and edit phylogenetic trees.
If started from the command line with filename as an argument, seaview
will open the alignment or tree stored in filename and display/draw it
on screen. Filename can be in any of the mase, clustal, phylip, msf,
fasta, or nexus alignment formats or in the Newick tree format.
OPTIONS
-fast
Suppresses double buffering for display. This should only
accelerate display on very slow systems.
-fontsize n
Sets the font size to n.
FILES
$HOME/.seaviewrc holds the user´s configuration for SeaView.
SEE ALSO
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/doc/seaview/seaview.html.
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.
SeaView usees some components of the PHYLIP package, see
‘http://evolution.genetics.washington.edu/phylip.html’.
REFERENCE
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.
AUTHORS
Manolo Gouy <mgouy@biomserv.univ-lyon1.fr>
Upstream author of SeaView.
Stéphane Bortzmeyer <bortzmeyer@debian.org>
Wrote this manpage in DocBook XML for the Debian distribution.
Charles Plessy <plessy@debian.org>
Updated this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
Copyright © 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005,
2006, 2007, 2008, 2009 Manolo Gouy
Copyright © 1999 Stéphane Bortzmeyer
Copyright © 2006, 2007, 2008, 2009 Charles Plessy
SeaView is released under the GNU General Public Licence, with a
special permission to use some source files from the PHYLIP package.
Because these files are used, you are not allowed generate revenue with
SeaView.
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
version 2 can be found in /usr/share/common-licenses/GPL-2.