Allignements visualization

Francois JEANMOUGIN pingouin at crystal.u-strasbg.fr
Wed Apr 30 02:11:25 EST 1997

In article <slrn5mcugn.o4k.aiyar at ebv.oncology.wisc.edu>,
	aiyar at ebv.oncology.wisc.edu () writes:
> On 29 Apr 1997 10:41:45 -0700,
> Matteo Turri (turrim at kispi.unizh.ch) wrote:
>>            I use Clustalw to align my protein sequences; I'm looking for a
>>software that provides flexible tool for sequences allignements
>>visualization, something that will shade the regions of similarity and
> I use a program called SeaView for this purpose.  It works very
> well with the output from Clustalx, a more recent version of
> Clustalw.  Seaview is available from biom3.univ-lyon1.fr under
> the directory /pub/mol_phylogeny/seaview

	And ClustalX from :

	Don't be confuse by the name, it does NOT require Xwindow
interface. It uses the vibrant libraries and is available for
the most popular platforms (Most unix, Mac and MS).
	Also, playing with the colprot.par and colprint.par files
can make a pretty good output in postscript. The postscript output
is a new feature of ClustalX also.

	For those who are using phylowin or seaview from a
clustal output, if you had to compile clustal, set
#define MAXNAMES 10
in the clustalw.h file.
This should be the default (I have to check...).
Else some error in seaview and phylowin display were reported
(spaces in the alignment...).
Sorry for this obscur part of the Clustal format definition.
If you sea such problems and can't recompile clustal, just save
your alignment in another format that seaview or phylowin can read
(GDE or MSF format, if I remember well).

Francois Jeanmougin
Service de bioinformatique / bioinformatics service
IGBMC BP 163 67404 Illkirch France
tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr
"C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun." (Thiefaine)

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