Hi Xianjun, We have a help page for this which can be found here: http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy Essentially, Apache will act as a proxy to your Galaxy instance. It is probably not a good idea to leave Galaxy anywhere in your web server's DocumentRoot since this would expose things that should not be accessible directly. --nate

Hi David, Due to variations between genomes, there are often more than one MAF block per region. You can however, have 1 stitched FASTA block per region: Start with your BED file. Go to Fetch Alignments, select Stitch MAF Blocks Tool. Set Choose Intervals to your BED file. Select your Desired MAF source from the locally cached alignments or alignments in your History. Select desired Species. Click Execute. This new file will now have 1 FASTA alignment block per region with the total number of sequences equaling (# of regions) x (# of species). Dan