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Updated: Oct 11, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Trivial minimization of extra-steps under dynamic homology
Abstract:
Farris (1983) stated that the rationale of the parsimony criterion was to minimize extra (i.e. non-minimal) steps. For traditional characters, this is equivalent to minimizing total steps (i.e. length). Under dynamic homology (sensu Wheeler, 2001), this identity is broken. Here, it is shown that extra steps (but not total) can be minimized trivially (to zero) for all data sets on all trees when insertion-deletion events are considered. © The Willi Hennig Society 2011.
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