Making gif's of dendrograms, UNIX ?

Francois Jeanmougin pingouin at chouchen.u-strasbg.fr
Thu Dec 4 02:56:55 EST 1997


In article <learn-0312970851160001 at tench.microbiol.washington.edu>,
	learn at u.washington.edu (Jerry Learn) writes:

> I concur with François' caveats about using the guide tree from clustal as
> a phylogenetic tree.

	Oh! Thanks ;-). Also, I don't want Clustal users to be flamed by
reviewers...

[...]
> The clustal package has the added feature of producing a NJ phylogram with
> bootstrap values at the nodes.  But as far as I know treetool is the only
> UNIX program
> <ftp://rdp.life.uiuc.edu/pub/RDP/programs/TreeTool>(SunOS/Solaris only)
> that can be used to visualize these trees.

	hmmm. I didn't check so much, but the Macintosh TreeView also
works well here. In fact, the trees are in standard Phylip format
(we feel that the phylip format is standard, it is easy to
use, read and manipulate, we choose it for the guide tree also),
so all the Phylip compatible programs should be able to read the
NJ trees.

> And as François suggests, if you are serious about constructing
> phylogenetic trees get programs (PAUP) or packages (PHYLIP) that
> specialize in phylogenetic reconstruction.  PHYLIP is available for free
> from <ftp://evolution.genetics.washington.edu/pub/phylip>.

	And PAUP was recently included in GCG9.1 (Just hard to manage here
between GCG8.1 with EGCG and GCG9 with PAUP. Quite confusing for users...).
 
> Also note that the URLs given for the HTML documentation will not work in
> most places -- try these instead:

	Ooooouuups. I didn't check. #?%µ££%% Netscape!

> <http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/Top.html> for the command
> line version
> <http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html> for the windowed
> version

	Yep, those are the good URLs, but there is probably a fast mirror
around your location. Also the ClustalX one is just a page (no image,
just tables), you can save as source and use it locally.

> Best of Luck,
> Jerry Learn

	Thanks for correcting the mistakes.
							François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France




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