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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.
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