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 51 articles )

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  1. Long, Colby; Kubatko, Laura: Identifiability and reconstructibility of species phylogenies under a modified coalescent (2019)
  2. Monod, Anthea; Kališnik, Sara; Patiño-Galindo, Juan Ángel; Crawford, Lorin: Tropical sufficient statistics for persistent homology (2019)
  3. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  4. Whidden, Chris; Iv, Frederick A. Matsen: Efficiently inferring pairwise subtree prune-and-regraft adjacencies between phylogenetic trees (2018)
  5. Bartoszek, Krzysztof; Glémin, Sylvain; Kaj, Ingemar; Lascoux, Martin: Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations (2017)
  6. Didier, Gilles: Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction (2017)
  7. Jansson, Jesper; Li, Zhaoxian; Sung, Wing-Kin: On finding the Adams consensus tree (2017)
  8. Domenach, Florent; Tayari, Ali: DASACT: a decision aiding software for axiomatic consensus theory (2016)
  9. Royer-Carenzi, Manuela; Didier, Gilles: A comparison of ancestral state reconstruction methods for quantitative characters (2016)
  10. Urheim, Ellen; Ford, Eric; St. John, Katherine: Characterizing local optima for maximum parsimony (2016)
  11. Hoyal Cuthill, Jennifer: The size of the character state space affects the occurrence and detection of homoplasy: modelling the probability of incompatibility for unordered phylogenetic characters (2015)
  12. Bogdanowicz, Damian; Giaro, Krzysztof: On a matching distance between rooted phylogenetic trees (2013)
  13. Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian: \textscFlipCutsupertrees: towards matrix representation accuracy in polynomial time (2013)
  14. Dong, Jianrong; Fernández-Baca, David; McMorris, F. R.; Powers, Robert C.: An axiomatic study of majority-rule ((+)) and associated consensus functions on hierarchies (2011)
  15. Holder, Mark T.; Steel, Mike: Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts (2011)
  16. Luecking, Robert K.; Hodkinson, Brendan P.; Stamatakis, Alexandros; Cartwright, Reed A.: PICS-ord: Unlimited coding of ambiguous regions by pairwise identity and cost scores ordination (2011) ioport
  17. 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
  18. Dong, Jianrong; Fernández-Baca, David; McMorris, F. R.; Powers, Robert C.: Majority-rule (+) consensus trees (2010)
  19. Durand, Pierre M.; Hazelhurst, Scott; Coetzer, Theresa L.: Evolutionary rates at codon sites May be used to align sequences and infer protein domain function (2010) ioport
  20. JSumner, J. G.; Charleston, M. A.: Phylogenetic estimation with partial likelihood tensors (2010)

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