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SEAVIEW(1)			Seaview	Manual			    SEAVIEW(1)

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.

       St~A(C)phane 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 (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
       2005, 2006, 2007, 2008, 2009 Manolo Gouy
       Copyright (C) 1999 StA(C)phane Bortzmeyer
       Copyright (C) 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.

seaview	4.0			  05/27/2009			    SEAVIEW(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | FILES | SEE ALSO | REFERENCE | AUTHORS | COPYRIGHT

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