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The programs part of the Staden package provide a fully developed set
of DNA sequence assembly, editing, analysis and more.
Some of its features include:
GAP4 - Performs assembly, contig joining, assembly checking, repeat search,
experiment suggestion, read pair analysis and contig editing.
GAP5 - The new development version of Gap4, designed to work with the large
volumes of data attainable through the newer sequencing technologies.
PREGAP4 - Provides a graphical user interface to set up the processing
required to prepare trace data for assembly or analysis.
SPIN - Compares pairs of sequences in many ways, often presenting its results
graphically and has a sliding sequence window linked to the plots.
TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF trace files.
For more information and citing, visit Staden's web page and check the
"References" file in the documentation.
This requires io_lib and tklib.
Notes:
1) You should run the SlackBuild in real root environment (su -)!
2) Make sure you have Emacs and Tetex installed, as they are needed
to generate the documentation.
3) Slackware's TCL and TK sources are expected to be in /tmp at build
time. The SlackBuild will unpack them in the build directory and
create the necessary symlinks in /tmp. You can safely delete the
symlinks when the build is complete.
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