seaview1

Usage

Overview

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.