--->System couldn't file Clustalw

Isn't the file supposed to be called clustalw.exe? Does the error message really mention a file with a capital letter in the name?

I fear you have some basic file path/permission problem, with which I could scarcely help from afar, even if I knew Windows.

The way forward always starts with a minimal test.

In reply to Re^7: Can't run Clustalw through Bioperl by 1nickt
in thread Can't run Clustalw through Bioperl by dimitris852

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