FakII is not included as part of the Staden Package. It is available from Susan Miller ( susanjo@cs.arizona.edu ).
FakII
suite of programs to perform shotgun
assembly. Output will be placed in the fofn.assembly directory, where fofn
is the filename prefix listed in the "Files to Process" panel. The output is
in a format suitable for directed assembly within gap4. This can also be
performed by using the "Enter Assembly into Gap4" module.
graph
component of FakII, which is used to
find the initial overlaps between sequences.
For further details, see
section Assembly FAKII.
assemble
component of FakII, which is used
for determining the best construction of sequences from the overlap graph.