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
