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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 frequenciesExpand
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PERMUTATIONS
Permutations of finite sets play a central role in algebraic and enumerative combinatorics. In addition to having many interesting enumerative properties per se, permutations also arise in almostExpand
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Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups
Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost ofExpand
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Support Weighting
Previous weighting methods—including compatibility weighting—have assumed that homoplasy indicates unreliability, but this assumption does not seem to hold for large molecular data matrices.Expand
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Taxic Revisions
Parsimony analysis provides a straightforward way of assessing homology on a tree: a state shared by two terminals comprises homologous similarity if optimization attributes that state to all theExpand
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RASA Attributes Highly Significant Structure to Randomized Data
“Relative apparent synapomorphy analysis” (RASA), a method proposed as a statistical test of hierarchic structure in data, would better be called “relative apparent similarity analysis.” The methodExpand
Cycles
Intended to support three‐taxon analysis (3ta), the proposal that all character states be regarded as terminal would instead undercut that method. The same is true of the idea that cladistic methodsExpand
EXPLANATION
James S. Fan-is’, Mari Killersjii’, Victor A. Albert’, Marc Allard’, Ame Anderberg4, Brunella Bowditch5, Carol Bult6, James M. Carpenter’, Timothy M. Crowe*, Jan De Laetg, Kirk Fitzhugh”, DarrylExpand
Branch Lengths Do Not Indicate Support—Even in Maximum Likelihood
It is still common to see the branch lengths of “phylograms”1 interpreted as indicating support for groups. This is unfortunate, for it is easy to find cases in which long branches do not indicateExpand
Diagnostic Efficiency of Three‐Taxon Analysis
Matrices of three‐taxon statements (3ts) represent a transformation of original data in that they are calculated from normal data matrices. Normal matrices cannot be considered transformational (orExpand