$ENV{CLUSTALDIR} = 'C:\Program Files (x86)\ClustalW2';

Please look very carefully at the path. On my current machine, I have both /Program Files (x86)/ and just /Program Files/ directories. Almost all my Program Files are in the "plain" directory. Just one program lives in /Program Files (x86)/.

I can't say for sure whether this will help or not, but it is an anomaly that I noticed on this particular machine.

In reply to Re^7: Can't run Clustalw through Bioperl by Marshall
in thread Can't run Clustalw through Bioperl by dimitris852

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