Local Mode
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A local Multiple RNAAlignment mode for Stem Loc. Does not attempt to align the entire sequence (in contrast to Global Mode).
Local Mode can be used with the following options:
- Progressive Mode - greedy progressive alignment
- Liberal Mode - length of initial pairwise seed alignment is allowed to increase during progressive extension
- Conservative Mode - length of initial pairwise seed alignment is fixed
- Profile Mode - profiling alignment using Covariance Models
See also Global Mode.
-- Ian Holmes - 05 Apr 2005
