clustalw

Ron Kagan qdbio at pacbell.net
Wed Jan 13 14:24:26 EST 1999


Peter:

I use CLUSTALW 1.74 running on Solaris 2.5.1.  I run CLUSTALW from a shell
script: first I create the alignment (in my case, a profile alignment):

$CLUSTAL/clustalw -sequences -PROFILE1=$LOGS/final.aln -PROFILE2=$FSA/$fsaname
-PWDNAMATRIX=CLUSTALW -DNAMATRIX=CLUSTALW -outfile=$ALIGN/$alignfile

Then I create the tree from the alignment file:

$CLUSTAL/clustalw -infile=$ALIGN/$alignfile -tree -kimura -outputtree=nj
-outputtree=phylip -outputtree=dist


I hope this helps!

Ron Kagan



Peter Rogan wrote:

> I would like to generate a Neighbor-Joining tree from the command line using
> the Sun Solaris version of clustalw. The documentation says it's possible
> but the software ignores the command (other commands are not ignored,
> ie. -align). Does anyone have a suggestion?
>
> Pete Rogan





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