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.