Tree Searches Under Sankoff Parsimony

Algorithms to speed up tree searches under Sankoff parsimony are described. For T terminal taxa, an exact algorithm allows calculating length during searches T to 2T times faster than a complete down‐pass optimization. An approximate but accurate method is from 3T to 8T times faster than a down‐pass. Other algorithms that provide additional increases of speed for simple symmetrical transformation costs are described.

[1]  E. C. Zimmerman,et al.  Cladistic analysis, phylogeny and biogeography of the Hawaiian Platynini (Coleoptera: Carabidae) , 1998 .

[3]  David L. Swofford,et al.  Uneconomical Diagnosis of Cladograms: Comments on Wheeler and Nixon's Method for Sankoff Optimization , 1997 .

[4]  D. Penny,et al.  Branch and bound algorithms to determine minimal evolutionary trees , 1982 .

[5]  P. Goloboff.  A reanalysis of mygalomorph spider families (Araneae) , 1993 .

[6]  Wayne P. Maddison,et al.  Parsimony , Character-State Reconstructions , and Evolutionary Inferences , 2022 .

[7]  Pablo A. Goloboff,et al.  A revision of the South American spiders of the family Nemesiidae (Araneae, Mygalomorphae). Part 1, Species from Peru, Chile, Argentina, and Uruguay. Bulletin of the AMNH ; no. 224 , 1995 .

[8]  Pablo A. Goloboff,et al.  Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs , 1997 .

[9]  CHARACTER‐STATE WEIGHTING FOR DNA RESTRICTION SITE DATA: ASYMMETRY, ANCESTORS AND THE ASTERACEAE , 1996 .

[10]  D. Sankoff,et al.  Locating the vertices of a Steiner tree in arbitrary space , 1975 .

[11]  Joseph B. Kruskal,et al.  Time Warps, String Edits, and Macromolecules , 1999 .

[12]  James F. Smith.  Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL , 1993 .

[13]  Kevin C. Nixon,et al.  A Novel Method for Economical Diagnosis of Cladograms under Sankoff Optimization , 1994 .

[14]  P. Goloboff.  METHODS FOR FASTER PARSIMONY ANALYSIS , 1996 .

[15]  Pablo A. Goloboff,et al.  CHARACTER OPTIMIZATION AND CALCULATION OF TREE LENGTHS , 1993 .

[16]  David Sankoff,et al.  Locating the vertices of a steiner tree in an arbitrary metric space , 1975, Math. Program..