The PipTools Software Package   (all-Perl version)

Please Note:  These tools use new file formats for repeats, color underlays, and hyperlinked annotations which were already in use by PipMaker, and are now supported by Laj as well. For best compatibility, please be sure to use the latest version of Laj.

PipTools is a collection of small programs designed to help users of our PipMaker server to prepare their input files more conveniently. Both PipMaker and its interactive viewer, Laj, have powerful annotation capabilities, but taking full advantage of them requires submitting extra files containing precise locations of genes and exons, repeats, color underlays, hyperlinks to additional information, and so forth. Preparing and manipulating these files manually can be a tedious task, and so we provide this set of tools to facilitate the process. There are also a few tools for searching PipMaker's output that work with either the "raw blastz output" or the "concise textual form of the alignments".

These are simple, independent programs designed to be run on your own computer. They are distributed as source code under the GNU Public License, so you can change them if you want to (please see the "README" and "COPYING" files for details). This version of the tools is written entirely in Perl, so you will need a Perl interpreter to run them; this should be available for all common computing platforms. (We also have a mostly-C version of the PipTools, if you prefer that.)

The current PipTools distribution package is available for download as a compressed zip archive, .

The following documentation files are included:

Cathy Riemer and Matt Weirauch, November 2001