I would like to use MultiPipMaker for testing a genome alignment between two sequences, each sequence is in .fasta format, but the problem is that when I submit the couples of file that I need, the web browser sends an email that the blastz has timed out. Does anybody know why is the that?

The address of the program is:

http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker

and the sequences that I am obtaining are the supercontigs from Broad Institute: http://www.broadinstitute.org/annotation/genome/mycobacterium_tuberculosis_diversity/MultiDownloads.html

thanks