1SEAVIEW(1)                      Seaview Manual                      SEAVIEW(1)
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NAME

6       seaview - a multiplatform, graphical user interface for multiple
7       sequence alignment and molecular phylogeny.
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SYNOPSIS

10       seaview [filename]
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DESCRIPTION

13       seaview is the program that starts the SeaView GUI.
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15       SeaView is a graphical interface for multiple sequence alignment and
16       molecular phylogeny. It is able to read various alignment formats (MSF,
17       CLUSTAL, FASTA, PHYLIP, MASE, NEXUS) and the Newick tree format, and
18       allows one to manually edit the alignment, to run DOT-PLOT, CLUSTAL or
19       MUSCLE programs to locally improve the alignment, and also to compute,
20       draw and edit phylogenetic trees.
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22       If started from the command line with filename as an argument, seaview
23       will open the alignment or tree stored in filename and display/draw it
24       on screen. Filename can be in any of the mase, clustal, phylip, msf,
25       fasta, or nexus alignment formats or in the Newick tree format.
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OPTIONS

28       -fast
29           Suppresses double buffering for display. This should only
30           accelerate display on very slow systems.
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32       -fontsize n
33           Sets the font size to n.
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FILES

36       $HOME/.seaviewrc holds the user´s configuration for SeaView.
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SEE ALSO

39       The program is fully documented online. Press the "help" button in the
40       main window. On Debian systems, the text template for SeaView´s help
41       can be found in /usr/share/doc/seaview/seaview.html.
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43       Two multiple alignment programs can be called from whithin SeaView:
44       muscle(1) and clustalw(1).
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46       The home page of SeaView is
47       http://pbil.univ-lyon1.fr/software/seaview.html.
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49       SeaView usees some components of the PHYLIP package, see
50       ‘http://evolution.genetics.washington.edu/phylip.html’.
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REFERENCE

53       If you use SeaView in a published work, please cite the following
54       reference: Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and
55       Phylo_win, two graphic tools for sequence alignment and molecular
56       phylogeny. Comput. Applic. Biosci., 12, 543-548.
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AUTHORS

59       Manolo Gouy <mgouy@biomserv.univ-lyon1.fr>
60           Upstream author of SeaView.
61
62       Stéphane Bortzmeyer <bortzmeyer@debian.org>
63           Wrote this manpage in DocBook XML for the Debian distribution.
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65       Charles Plessy <plessy@debian.org>
66           Updated this manpage in DocBook XML for the Debian distribution.
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69       Copyright © 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005,
70       2006, 2007, 2008, 2009 Manolo Gouy
71       Copyright © 1999 Stéphane Bortzmeyer
72       Copyright © 2006, 2007, 2008, 2009 Charles Plessy
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74       SeaView is released under the GNU General Public Licence, with a
75       special permission to use some source files from the PHYLIP package.
76       Because these files are used, you are not allowed generate revenue with
77       SeaView.
78
79       You can redistribute and/or modify this manpage under same terms as
80       SeaView itself.
81
82       On Debian systems, the complete text of the GNU General Public License
83       version 2 can be found in /usr/share/common-licenses/GPL-2.
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88seaview 4.0                       05/27/2009                        SEAVIEW(1)
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