The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

  title={The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis},
  author={Kevin C Nixon},
  • 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… 
Parsimony analysis of phylogenomic datasets (II): evaluation of PAUP*, MEGA and MPBoot
This paper examines the implementation of parsimony methods in the programs PAUP*, MEGA and MPBoot, and compares them with TNT, and finds that bootstrapping with PAUP, MEGA or MPBoot can attribute strong supports to groups that have no support at all under any meaningful concept of support, such as likelihood ratios or Bremer supports.
Inferring large phylogenies: The big tree problem
Overall, the Order Primates has diversified at a constant rate of cladogenesis, though looked at in more detail the authors note, in agreement with earlier studies, a significantly elevated rate in the cercopithecines.
Efficient Tree Searches with Available Algorithms
  • G. Giribet
  • Biology
    Evolutionary bioinformatics online
  • 2007
The techniques discussed here apply to both major families of methods based on optimality criteria—parsimony and maximum likelihood—and allow the thorough analysis of complex data sets with hundreds to thousands of terminal taxa.
Sampling phylogenetic tree space with the generalized Gibbs sampler.
  • J. Keith
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 2015
Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)
The computationally most efficient and versatile parsimony software, TNT, is described, which can be used for phylogenetic and phylogenomic analyses, and a series of scripts that are specifically designed for the analysis of phylogenomic datasets are described.
Fast character optimization in parsimony phylogeny reconstruction
This paper describes an exact and fast algorithm to compute tree length and the algorithm can obtain great speedup for any data sets.
A structural EM algorithm for phylogenetic inference
This paper describes a new algorithm that uses Structural-EM for learning maximum likelihood trees, and proves that each iteration of this procedure increases the likelihood of the topology, and thus the procedure must converge.
Techniques for Analyzing Large Data Sets
The techniques described here have so far been used only for prealigned sequences, but they could be adapted for other methods of analysis, like the direct optimization method of Wheeler.


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
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
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
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
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    • 1988
    Winclada (beta) ver
    • 0.9. Published by the author, Ithaca, NY. [Available at]
    • 1999
    PAUP: Phylogenetic Analysis Using Parsimony, ver
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