Making gif's of dendrograms, UNIX ?

Jerry Learn learn at u.washington.edu
Wed Dec 3 11:51:00 EST 1997


In article <6633sd$o2j at news.u-strasbg.fr>, jeanmougin at igbmc.u-strasbg.fr wrote:

> > In article <Pine.GSO.3.96.971202105454.17675A-100000 at nature.berkeley.edu>,
> > Brian Osborne <bosborne at NATURE.BERKELEY.EDU> wrote:
> >>I am generating alignments and the associated
> >>dendrograms (*.dnd) using clustalw (command line).
> >>I would like to take the *.dnd file and make it into
> >>a GIF, again, from the command line. I've used
> >>Phylip, but this cannot make GIFs, as far as I
> >>can tell. One possibility would be to use Phylip
> >>to make a .ps file, then do a ps -> gif I suppose.
> >>Is there any utility that can do this directly,
> >>for UNIX?
> 
>         Well, I don't know what you really want to do with the .dnd file
> from Clustal, but I saw so much errors with the pileup.figure tree that
> I think I have to put a warning here :
>         The .dnd file generated by Clustal is NOT a phylogenetic tree.
> This tree is only made using % identity derived from the pairwise
> alignment and is used as a guide tree for the clustering alignement
> (generating clusters by using the nearest neighbours in the tree).
> We also found recently that we perhaps could use this tree to overweight
> a sequence in the alignement (making a sequence drive the alignment).
> We have to test it before documenting it, it's quite a hack ;-).
> 
>         As said in the Clustal documentation, please use the Phylip
> package if you are interested in tree.
> 
>         Clustal ftp update site:
>         ftp://ftp-igbmc.u-strasbg.fr/pub/
> 
>         HTML documentation (there are several mirrors, check altavista)
> http://www-igbmc/BioInfo/ClustalW/Top.html for the command line version
> http://www-igbmc/BioInfo/ClustalX/Top.html for the windowed version
> (courtesy from EMBnet/CMB Spain).
> 
>         Also, lot of details will appear in Nucleic Acid Research next week
> (last issue of 1997).
> 
I concur with François' caveats about using the guide tree from clustal as
a phylogenetic tree.  However, the current versions of clustal can be used
to produce neighbor-joining trees, once you have examined the alignment to
correct possible errors (this, of course, should be done before any
further analysis). 
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.

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>.

Also note that the URLs given for the HTML documentation will not work in
most places -- try these instead:

<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

Best of Luck,
Jerry Learn

Research Associate

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