man seaview (1): 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.

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 <[email protected]>

: Upstream author of SeaView.

Stéphane Bortzmeyer <[email protected]>

: Wrote this manpage in DocBook XML for the Debian distribution.

Charles Plessy <[email protected]>

: Updated this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

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.