Thanx a lot for your answers! I surely missed that part on the Clustalw.pm CLUSTALDIR variable. Ok, I'll set that up tonight and come back with the results. I will also check that SystemDrive env... But in all cases, I guess that the best thing to do is to set my server in a linux env right?...Julio
Ok, I solved the prob. As almut thought, the prob was with the environment variable CLUSTALDIR. What I needed to do was to set the env variable in the httpd.conf file. So I added the following line: