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TNT, a free program for phylogenetic analysis
TLDR
Through the use of a number of native commands and a simple but powerful scripting language, TNT allows the user an enormous flexibility in phylogenetic analyses or simulations.
TNT version 1.5, including a full implementation of phylogenetic morphometrics
TLDR
Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before, thus making phylogenetic analysis of landmarks feasible even on standard personal computers.
ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH
  • P. Goloboff
  • Medicine, Mathematics
    Cladistics : the international journal of the…
  • 1 March 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
Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima
TLDR
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.
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
Weighting against homoplasy improves phylogenetic analysis of morphological data sets
The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well
Continuous characters analyzed as such
Quantitative and continuous characters have rarely been included in cladistic analyses of morphological data; when included, they have always been discretized, using a variety of ad hoc methods. As
Methods for Quick Consensus Estimation
A method that allows estimating consensus trees without exhaustive searches is described. The method consists of comparing the results of different independent superficial searches. The results of
Regular ArticleEstimating Character Weights during Tree Search
—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 trees
Areas of endemism: an improved optimality criterion.
TLDR
Algorithms to evaluate areas of endemism under this criterion are discussed, and implemented in a computer program (NDM), which allow evaluation of much larger data sets.
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