TNT: Tree Analysis Using New Technology

@article{Giribet2005TNTTA,
  title={TNT: Tree Analysis Using New Technology},
  author={Gonzalo Giribet},
  journal={Systematic Biology},
  year={2005},
  volume={54},
  pages={176-178}
}
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1,179 Citations
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References

SHOWING 1-10 OF 18 REFERENCES

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.

The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

With the ratchet, Goloboff's NONA, and existing computer hardware, data sets that were previously intractable or required months or years of analysis with PAUP* can now be adequately analyzed in a few hours or days.

ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

  • P. Goloboff
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 1993
Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non‐iterative and does not require independent estimations of weights. It is based on searching…

Methods for Quick Consensus Estimation

A way to collapse branches considering suboptimal trees is described, which can be extended as a measure of relative support for groups; the relative support is based on the Bremer support, but takes into account relative amounts of favorable and contradictory evidence.

Improvements to resampling measures of group support

Several aspects of current resampling methods to assess group support are reviewed. When the characters have different prior weights or some state transformation costs are different, the frequencies…

Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima

New methods for parsimony analysis of large data sets are presented, including sectorial searches, tree‐drifting, and tree‐fusing which find a shortest tree in less than 10 min and perform well in other cases analyzed.

A CLADISTIC ANALYSIS OF THE CYPHOPHTHALMID GENERA (OPILIONES, CYPHOPHTHALMI)

A phylogenetic analysis of the genera of Cyphophthalmi is undertaken by studying 32 morphological characters in 43 species representing all families and most genera, and molecular characters strongly support the monophyly of Troglosironidae + Neogoveidae.

NEXUS: an extensible file format for systematic information.

The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program.

THE LIMITS OF AMINO ACID SEQUENCE DATA IN ANGIOSPERM PHYLOGENETIC RECONSTRUCTION

  • K. Bremer
  • Biology
    Evolution; international journal of organic evolution
  • 1988
Cladistic analysis of amino acid sequence data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated.

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

  • J. Felsenstein
  • Economics
    Evolution; international journal of organic evolution
  • 1985
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.