PipMaker and MultiPipMaker

PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ``percent identity plot'', or ``pip'' for short. MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.

These pages are under constant revision, and are located on several physical systems. Please be careful to bookmark only our published URLs, http://bio.cse.psu.edu/, and http://bio.cse.psu.edu/pipmaker, otherwise your links to internal pages may go stale.

PipMaker generates graphical output as a PDF document by default, or optionally as a PostScript document. If your system doesn't already have one, you may want to fetch and install a free PostScript/PDF viewer. One such tool is manufactured by Aladdin Inc, called Ghostscript. The Aladdin web page has instructions for attaching it to Netscape or MS Internet-Explorer. Another such tool is Acroread, from Adobe. At the present time, Acroread has better support for hyperlinks in PDF files, which PipMaker uses.

We have had reports of bugs in some versions of Microsoft Internet Explorer. If you have trouble, try using Netscape, or some other web browser.

If you publish results obtained using PipMaker, please cite Schwartz et al., Genome Research 10:577-586, April 2000.

Documentation and examples can be found here:

The application itself can be found here:

Download the source (beta version) pipmaker-2011-08-12-01.tar.bz2

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Development and maintenance of PipMaker is supported by grant HG02238 from the National Human Genome Research Institute.

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