MultiPipMaker processes the contents of the same files as does Advanced PipMaker, except that more than two sequences can be submitted. In addition, the user is asked to provide a name for each sequence; these names should be limited to a single word that containes only letters, digits and the underscore character. Moreover, the user may need to be more careful with FastA header lines in the sequence files; each file should begin with a unique FastA header line, and the first word on each line (i.e., up to the first blank) should be kept simple.
Besides producing a pip that PipMaker users should find easy to interpret, MultiPipMaker offers two new output options. (Be warned that both of these files are so large that some email programs may refuse to accept them.) The first option is for a PDF file giving a nucleotide-level view of a multiple alignment of the submitted sequences. This alignment displays the exons, interspersed repeats, underlays and annotations in a manner that is appropriate for the high-resolution view. The second output option is for a text file giving the multiple alignment. This file is not intended for direct human inspections, but is to be read by tools (which will be made available at the MultiPipMaker website) that extract various kinds of information, such as conserved regions with a user-specified level of information content, or regions that match a user specified nucleotide pattern.
Follow this link to see an example of MultiPipMaker, with sample input and output files.