SEAVIEW(1)

📦 version 5.1+20251106, in debian bookworm, debian trixie, fedora 43, fedora 44, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ SEAVIEW 💅 — the seaview manual page, bestie edition ✨

okay so we're doing the SEAVIEW(1) page from the Seaview Manual and honestly? iconic. let's go 🧚

🌸 NAME 🌸

seaview — a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

🦋 SYNOPSIS 🦋

seaview [filename]

💖 DESCRIPTION 💖

so seaview is literally the program that starts the SeaView GUI. that's it. that's the job. main character energy from the jump 👑

SeaView is a graphical interface for multiple sequence alignment and molecular phylogeny. she can read a whole lil buffet of alignment formats — MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS — plus the Newick tree format. and she lets you:

  • manually edit the alignment ✏️
  • run DOT-PLOT, CLUSTAL or MUSCLE programs to locally improve the alignment 🔧
  • compute, draw and edit phylogenetic trees 🌳

If you start her 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. no cap. 🫶

✨ OPTIONS ✨

  • -fast — suppresses double buffering for display. lowkey this should only accelerate display on very slow systems, so don't come for her if you don't notice a thing bestie 💀
  • -fontsize n — sets the font size to n. that's the vibe check, n is the number, go off 🎀

🎀 FILES 🎀

$HOME/.seaviewrc holds the user´s configuration for SeaView. yes, it's a dotfile, it's giving home-directory-core 🏠✨

🌈 SEE ALSO 🌈

the program is fully documented online. press the "help" button in the main window, babes, it's right there 🫶

On Debian systems, the text template for SeaView´s help can be found in /usr/share/doc/seaview/seaview.html. (yes that's a real path, write it down 📝)

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 — fr fr, cite it, it's the least you can do 🙏:

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. the OG 🐐
  • 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 © 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. okay bestie that's a real rule, don't be sneaky 💀

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.

k that's the whole page, you ate it, no crumbs left 🌸✨

and for the cute lil sign-off: this was seaview 4.0, dated 05/27/2009 💅 mwah, go align something, bestie 🦋

📦 where this page comes from