#2 postnuc/postpro problems

open
nucmer (5)
5
2005-06-01
2005-06-01
Adam Phillippy
No

_should use the MUM overlap information to determine
tandem copies rather than throw out the overlap
_when reading in clusters, matches to the concated
reference that (by chance) get cluster across the
concat point are made into their own clusters rather
than being discarded
_gap penalties are non-optimal
_symmetry problems in mgaps
_extension overrun problem misses nearby clusters
_extension overflow may terminate alignment prematurely

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