clustalw matrice

Fred Opperdoes opperdoes at trop.ucl.ac.be
Mon Apr 30 03:58:47 EST 2001

olivier wrote:

> Hello,
> Does somebody know how to creat a
> matrice distance for clustalw.
> Thanks.

Dear Olivier,
To create a distance matrix in ClustalW you proceed as follows. Firts
import or create a multiple alignment in Clsutal. When done, go to the
menu item 4. "Phylogenetic tree". Select "Exclude positions with Gaps =
ON "and "Correct for muliple substitutions = On" if you want a PAM
matrix or select "OFF" in the case you want the distances expressed as
simple percentages. Now go to the menu item 6. "output options format"
and select 3. "Toggle Phylip distance matrix output = ON". Now go back
to the Phylogenetic tree menu and and select 4. "Draw tree now". In your
directory you will find a file with the suffix ".dst", which is your
distance matrix. If you also selected "Toggle Phylip tree format =ON"
you will also find a tree file in your directory as well.
Good luck.


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