Mulitple alignment editor

Nicolas Nicolas
Mon Oct 28 09:06:58 EST 1996

In article <3274b50c.0 at cisun2000.unil.ch>, khofmann at isrec-sun1.unil.ch (Kay Hofmann) writes:
> Guy Perriere (perriere at biomserv.univ-lyon1.fr) wrote:
> : Ewan Birney <birney at sanger.ac.uk> writes:
> : >As always, I am looking for a multiple alignment editor
> : >which works on SGI/alpha. 
> : Mano Gouy in our department has developed SeaView, a very good multiple
> : alignment editor that runs on SGI, Alpha, Sun, HP/UX and AIX. You can
> : find informations about this program at URL:
> :        http://acnuc.univ-lyon1.fr/phylogeny/seaview.html
> While this editor certainly looks nice, I understand that it can
> save the alignments only in a strange 'mase' format and works with none
> of the standard formats (it can read MSF, though).
> This makes seaview not very convenient for people who have to 
> integrate the alignment editor into a set of already existing software.
> And a new sequence format is the last thing we need right now.

This is not true. Seaview can read and write 5 file formats, namely MASE,
FASTA, MSF, CLUSTAL, PHYLIP. By the way, the MASE format is not new: it
was first designed by Faulkner and Jurka (1988, Trends Biochem Sci 13-321).
It was found convenient because it allows the storage of comments for the
whole file and for each sequences. That's partly why we chose it as the default
format in both SEAVIEW and PHYLO_WIN tools.

Nicolas Galtier
Laboratoire de Biometrie, Genetique et biologie des Populations
Universite C. Bernard Lyon1

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