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). Most of the tools are written in C, so you will need an ANSI C compiler in order to install them, but a few are written in Perl, so you will need a Perl interpreter for those. Both C and Perl should be available for all common computing platforms.
The current PipTools distribution package is available for download as a compressed zip archive, piptools.zip .
The following documentation files are included: