ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

@article{Goloboff1993ESTIMATINGCW,
  title={ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH},
  author={Pablo A. Goloboff},
  journal={Cladistics},
  year={1993},
  volume={9}
}
  • P. Goloboff
  • Published 1 March 1993
  • Medicine, Mathematics
  • Cladistics
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 trees with maximum total fit, with character fits defined as a concave function of homoplasy. Then, when comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated, during the analysis, as… 
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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…
On defining a unique phylogenetic tree with homoplastic characters.
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The present finding allows creating matrices which have as much homoplasy as possible for the most parsimonious or likely tree to be predictable, and examination of these matrices with hill-climbing search algorithms provides additional evidence on the (lack of a) necessary relationship between Homoplasy and the ability of search methods to find optimal trees.
A reconsideration of inapplicable characters, and an approximation with step‐matrix recoding
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This paper proposes an equivalent but more intuitive formulation of homoplasy, x‐transformations, based on counting the number of changes into each separate state, and presents a simple convention for naming characters, which TNT can use to automatically convert the original data into a step‐matrix form and set the proper transformation costs.
PARSIMONY AND WEIGHTING: A REPLY TO TURNER AND ZANDEE
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    Cladistics : the international journal of the Willi Hennig Society
  • 1995
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It is shown that there is no basis for Turner and Zandee’s criticism of the Goloboff method of weighting, and that the “new” findings presented are not such-they are well-known facts-and that they constitute in themselves no evidence against the method, or any other.
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A reasonable justification for an a priori weighting scheme within a falsificationist approach to phylogeny is provided, which demonstrates the indispensable necessity of its application.
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Analysis of a variety of simulated datasets shows that methods for coding continuous characters can lead to the generation of well-resolved trees that do not reflect a phylogenetic signal, and provides a method to avoid this potential bias.
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TLDR
TreeSearch is an R package for phylogenetic analysis, optimized for morphological datasets, designed to help a user to improve the quality of datasets through critical review of underpinning character codings and to obtain additional information from results.
A Corrected Parsimony Criterion for Reconstructing Phylogenies
TLDR
A corrected parsimony criterion for reconstructing phylogenies is presented, which states that character rather than step is the most fundamental unit and the most parsimonious tree should maximize the sum or average of the phylogenetic signals, quantified by retention index, contributed by each character.
BRANCH SUPPORT AND TREE STABILITY
Abstract— Branch support is quantified as the extra length needed to lose a branch in the consensus of near‐most‐parsimonious trees. This approach is based solely on the original data, as opposed to…
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