Making gif's of dendrograms, UNIX ?
pingouin at chouchen.u-strasbg.fr
Wed Dec 3 03:05:33 EST 1997
In article <662cul$31h$1 at nntp3.u.washington.edu>,
joe at evolution.genetics.washington.edu (Joe Felsenstein) writes:
> 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,
> There are utilities (I think in the PBMPlus package) called
> ps2ppm and ppmtogif that could do it.
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:
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).
François Jeanmougin | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
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