I Just made it work! Steps to make it work:

1)copy the clustalw2.exe

2)paste it on your e.g. Desktop

3)Rename it to clustalw.exe

4)Give the $ENV{CLUSTALDIR}the new path to clustalw.exe

and it works!

(at first tried to rename the basic clustalw2.exe of 'C:\Program Files (x86)\ClustalW2' but didn't work)

Thanks everybody for your help and your time! Have a nice day!

In reply to Re^13: Can't run Clustalw through Bioperl by dimitris852
in thread Can't run Clustalw through Bioperl by dimitris852

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