PipMaker instructions for rVista users:

• Use Advanced PipMaker
• Submit first and second sequence files
• Indicate your email address (so you can receive a link to download results)
• Select Chaining option. rVista does not work WITHOUT chaining
• Select Traditional textual form of the alignments
• Deselect Split second sequence into contigs on NN...
• Select Get results via: WWW
• Submit the request

After your receive an email from PipMaker save the file called blastz output, verbose (text)
as text
Submit text file to rVista