The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

@article{Nixon1999ThePR,
  title={The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis},
  author={Kevin C Nixon},
  journal={Cladistics},
  year={1999},
  volume={15}
}
  • K. Nixon
  • Published 1 December 1999
  • Computer Science
  • Cladistics
The Parsimony Ratchet 1 is presented as a new method for analysis of large data sets. The method can be easily implemented with existing phylogenetic software by generating batch command files. Such an approach has been implemented in the programs DADA (Nixon, 1998) and Winclada (Nixon, 1999). The Parsimony Ratchet has also been implemented in the most recent versions of NONA (Goloboff, 1998). These implementations of the ratchet use the following steps: (1) Generate a starting tree (e.g., a… 
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References

SHOWING 1-9 OF 9 REFERENCES
Analyzing large data sets: rbcL 500 revisited.
In 1993, Mark Chase and 41 coauthors published phylogenetic analyses of two very large data sets of nucleotide sequenc? es of the chloroplast gene rbcL, which en? codes the large subunit of ribulose
A Report on “One Day Symposium on Numerical Cladistics”
  • I. Horovitz
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 1999
TLDR
A recent symposium on numerical cladistics addressed novel methods for searching tree space, applications of randomizations in cladistic analysis, and data management, and modifications to parsimony jackknifing that improved its accuracy when compared to normal heuristic searches.
The discovery and importance of multiple islands of most
TLDR
The set of most-parsimonious trees for a data matrix may include several distinct classes (islands) of trees, and trees in different islands may have different implications for character evolution, and for this reason should be sought.
Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL
TLDR
Two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups indicate that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling.
Dada ver
  • 1.9. Software and manual. Published by the author, Trumansburg, NY.
  • 1998
from less than 200 trees collected from four ratchet runs. Thus, collecting ratchet trees in much
    Hennig86
    • Software and manual. Published by the author, Port Jefferson, NY.
    • 1988
    Winclada (beta) ver
    • 0.9. Published by the author, Ithaca, NY. [Available at http://www.cladistics.com]
    • 1999
    PAUP: Phylogenetic Analysis Using Parsimony, ver
    • 3.0. Illinois Natl. Hist. Surv., Champaign, IL.
    • 1990