The programs part of the Staden package provide an excellent and 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.
Notes:
1) You should run the SlackBuild in real root environment (su -)!
2) Make sure you have Emacs and Tetex installed at build time.
3) Although unsupported at the moment, SPIN can provide a GUI for the
EMBOSS suite programs. If you want to give it a try, run as root
"create_emboss_files" (EMBOSS should be installed, of course). This
generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl,
so remember to manually clean them if you later uninstall staden.
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