PAUP*: phylogenetic analysis under parsimony. PAUP* version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, Windows, UNIX/VMS, or DOS-based formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proven to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version represents a great improvement over its predecessors. In addition, the speed of the branch-and-bound algorithm has been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure. These, along with many other improvements, will make PAUP* 4.0 an even more indispensable tool in comparative biological analysis than were previous editions of the program and manual. PAUP* 4.0 and MacClade 3 use a common data file format (NEXUS), allowing easy interchange of data between the two programs.

References in zbMATH (referenced in 30 articles )

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  1. Bartoszek, Krzysztof; Glémin, Sylvain; Kaj, Ingemar; Lascoux, Martin: Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations (2017)
  2. Didier, Gilles: Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction (2017)
  3. Domenach, Florent; Tayari, Ali: DASACT: a decision aiding software for axiomatic consensus theory (2016)
  4. Royer-Carenzi, Manuela; Didier, Gilles: A comparison of ancestral state reconstruction methods for quantitative characters (2016)
  5. Urheim, Ellen; Ford, Eric; St. John, Katherine: Characterizing local optima for maximum parsimony (2016)
  6. Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian: FlipCut supertrees: towards matrix representation accuracy in polynomial time (2013)
  7. Dong, Jianrong; Fernández-Baca, David; McMorris, F.R.; Powers, Robert C.: An axiomatic study of majority-rule $(+)$ and associated consensus functions on hierarchies (2011)
  8. Carmel, Liran; Wolf, Yuri I.; Rogozin, Igor B.; Koonin, Eugene V.: EREM: parameter estimation and ancestral reconstruction by expectation-maximization algorithm for a probabilistic model of genomic binary characters evolution (2010) ioport
  9. Dong, Jianrong; Fernández-Baca, David; McMorris, F.R.; Powers, Robert C.: Majority-rule (+) consensus trees (2010)
  10. Mariadassou, M.; Bar-Hen, A.: Concentration inequality for evolutionary trees (2009)
  11. Steel, Mike; Székely, László A.: An improved bound on the maximum agreement subtree problem (2009)
  12. Amenta, Nina; Godwin, Matthew; Postarnakevich, Nicolay; John, Katherine St.: Approximating geodesic tree distance (2007)
  13. Brooks, Daniel R.; Erdem, Esra; Erdoğan, Selim T.; Minett, James W.; Ringe, Don: Inferring phylogenetic trees using answer set programming (2007)
  14. Lin, Yu-Min; Fang, Shu-Cherng; Thorne, Jeffrey L.: A tabu search algorithm for maximum parsimony phylogeny inference (2007)
  15. Picardi, Ernesto; Quagliariello, Carla: EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing (2006)
  16. Cai, Zhipeng; Heydari, Maysam; Lin, Guohui: Clustering binary oligonucleotide fingerprint vectors for DNA clone classification analysis (2005)
  17. Du, Zhihua; Lin, Feng; Roshan, Usman W.: Reconstruction of large phylogenetic trees: a parallel approach (2005)
  18. Nakhleh, Luay; Ruths, Derek; Wang, Li-San: RIATA-HGT: A fast and accurate heuristic for reconstructing horizontal gene transfer (2005)
  19. Bryant, David: A lower bound for the breakpoint phylogeny problem (2004)
  20. Miyakawa, Kampei; Narushima, Hiroshi: Lattice-theoretic properties of MPR-posets in phylogeny (2004)

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