Journal ArticleDOI
The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
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TLDR
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.About:
This article is published in Cladistics.The article was published on 1999-12-01. It has received 1564 citations till now. The article focuses on the topics: Tree (data structure) & Set (abstract data type).read more
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TNT, a free program for phylogenetic analysis
TL;DR: 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.
Journal ArticleDOI
phangorn: Phylogenetic analysis in R
TL;DR: Phangorn is a package for phylogenetic reconstruction and analysis in the R language that offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation.
Journal ArticleDOI
Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects
Joan Pons,Joan Pons,Timothy G. Barraclough,Timothy G. Barraclough,Jesús Gómez-Zurita,Jesús Gómez-Zurita,Anabela Cardoso,Anabela Cardoso,Daniel P. Duran,Steaphan Hazell,Steaphan Hazell,Sophien Kamoun,William D. Sumlin,Alfried P. Vogler,Alfried P. Vogler +14 more
TL;DR: In this paper, the authors use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia, using a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level evolutionary processes.
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The amphibian tree of life
Darrel R. Frost,Taran Grant,Taran Grant,Julián Faivovich,Julián Faivovich,Raoul H. Bain,Alexander Haas,Célio F. B. Haddad,Rafael O. de Sá,Alan Channing,Mark Wilkinson,Stephen C. Donnellan,Christopher J. Raxworthy,Jonathan A. Campbell,Boris L. Blotto,Paul E. Moler,Robert C. Drewes,Ronald A. Nussbaum,John D. Lynch,David M. Green,Ward C. Wheeler +20 more
TL;DR: A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one, based on the largest phylogenetic analysis of living Amphibia so far accomplished, and many subsidiary taxa are demonstrated to be nonmonophyletic.
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TNT version 1.5, including a full implementation of phylogenetic morphometrics.
TL;DR: 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.
References
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Book
PAUP* 4.0 : Phylogenetic Analysis Using Parsimony
TL;DR: PAUP* 4.0 Beta is a major upgrade of the bestselling software for the inference of evolutionary trees, for use in Macintosh or Windows/DOS-based formats.
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Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL.
TL;DR: 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.
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The discovery and importance of multiple islands of most-parsimonious trees
TL;DR: In this article, the set of most parsimonious trees for a data matrix may include several distinct classes (islands) of trees, each one differing from the next by a single rearrangement of branches.
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Analyzing large data sets: rbcL 500 revisited.
TL;DR: In 1993, Mark Chase and 41 coauthors published phylogenetic analyses of two very large data sets of nucleotide sequenc?
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A Report on “One Day Symposium on Numerical Cladistics”
TL;DR: 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.