Bioinformatics Vol. 17 no. 12 2001
Pages 1246-1247
© 2001 Oxford University Press
Applications Note |
CONSEL: for assessing the confidence of phylogenetic tree selection
The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minatoku, Tokyo 106-8569, Japan
Received on May 30, 2000
; revised on June 20, 2000
; accepted on July 2, 2000
Summary: CONSEL is a program to assess the confidence of the tree selection by giving the p-values for the trees. The main thrust of the program is to calculate the p-value of the Approximately Unbiased (AU) test using the multi-scale bootstrap technique. This p-value is less biased than the other conventional p-values such as the Bootstrap Probability (BP), the Kishino–Hasegawa (KH) test, the Shimodaira–Hasegawa (SH) test, and the Weighted Shimodaira–Hasegawa (WSH) test. CONSEL calculates all these p-values from the output of the phylogeny program packages such as Molphy, PAML, and PAUP*. Furthermore, CONSEL is applicable to a wide class of problems where the BPs are available.
Availability: The programs are written in C language. The source code for Unix and the executable binary for DOS are found at http://www.ism.ac.jp/~shimo/
Contact: shimo{at}ism.ac.jp
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 Y. Takao, K. Mise, K. Nagasaki, T. Okuno, and D. Honda Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp. J. Gen. Virol., March 1, 2006; 87(Pt 3): 723 - 733. [Abstract] [Full Text] [PDF]
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A. G. B. Simpson, Y. Inagaki, and A. J. Roger Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of "Primitive" Eukaryotes Mol. Biol. Evol., March 1, 2006; 23(3): 615 - 625. [Abstract] [Full Text] [PDF]
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A. G. Collins, P. Schuchert, A. C. Marques, T. Jankowski, M. Medina, and B. Schierwater Medusozoan Phylogeny and Character Evolution Clarified by New Large and Small Subunit rDNA Data and an Assessment of the Utility of Phylogenetic Mixture Models Syst Biol, February 1, 2006; 55(1): 97 - 115. [Abstract] [Full Text] [PDF]
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M. J. Phillips, P. A. McLenachan, C. Down, G. C. Gibb, and D. Penny Combined Mitochondrial and Nuclear DNA Sequences Resolve the Interrelations of the Major Australasian Marsupial Radiations Syst Biol, February 1, 2006; 55(1): 122 - 137. [Abstract] [Full Text] [PDF]
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C. L. Nesbo, M. Dlutek, and W. F. Doolittle Recombination in Thermotoga: Implications for Species Concepts and Biogeography Genetics, February 1, 2006; 172(2): 759 - 769. [Abstract] [Full Text] [PDF]
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A. J Baker, S. L. Pereira, O. P Haddrath, and K.-A. Edge Multiple gene evidence for expansion of extant penguins out of Antarctica due to global cooling Proc R Soc B, January 7, 2006; 273(1582): 11 - 17. [Abstract] [Full Text] [PDF]
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E. T. Steenkamp, J. Wright, and S. L. Baldauf The Protistan Origins of Animals and Fungi Mol. Biol. Evol., January 1, 2006; 23(1): 93 - 106. [Abstract] [Full Text] [PDF]
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D. H. Bos and B. Waldman Evolution by Recombination and Transspecies Polymorphism in the MHC Class I Gene of Xenopus laevis Mol. Biol. Evol., January 1, 2006; 23(1): 137 - 143. [Abstract] [Full Text] [PDF]
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U. Gophna, J. R. Thompson, Y. Boucher, and W. F. Doolittle Complex Histories of Genes Encoding 3-Hydroxy-3-methylglutaryl-CoenzymeA Reductase Mol. Biol. Evol., January 1, 2006; 23(1): 168 - 178. [Abstract] [Full Text] [PDF]
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R. B. Bevan, B. F. Lang, and D. Bryant Calculating the Evolutionary Rates of Different Genes: A Fast, Accurate Estimator with Applications to Maximum Likelihood Phylogenetic Analysis Syst Biol, December 1, 2005; 54(6): 900 - 915. [Abstract] [Full Text] [PDF]
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V. Hampl, D. S. Horner, P. Dyal, J. Kulda, J. Flegr, P. G. Foster, and T. M. Embley Inference of the Phylogenetic Position of Oxymonads Based on Nine Genes: Support for Metamonada and Excavata Mol. Biol. Evol., December 1, 2005; 22(12): 2508 - 2518. [Abstract] [Full Text] [PDF]
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X. Shi, H. Gu, E. Susko, and C. Field The Comparison of the Confidence Regions in Phylogeny Mol. Biol. Evol., November 1, 2005; 22(11): 2285 - 2296. [Abstract] [Full Text] [PDF]
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H. Brinkmann, M. van der Giezen, Y. Zhou, G. P. de Raucourt, and H. Philippe An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics Syst Biol, October 1, 2005; 54(5): 743 - 757. [Abstract] [Full Text] [PDF]
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T. R. Bachvaroff, M. V. Sanchez Puerta, and C. F. Delwiche Chlorophyll c-Containing Plastid Relationships Based on Analyses of a Multigene Data Set with All Four Chromalveolate Lineages Mol. Biol. Evol., September 1, 2005; 22(9): 1772 - 1782. [Abstract] [Full Text] [PDF]
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G. N. Eick, D. S. Jacobs, and C. A. Matthee A Nuclear DNA Phylogenetic Perspective on the Evolution of Echolocation and Historical Biogeography of Extant Bats (Chiroptera) Mol. Biol. Evol., September 1, 2005; 22(9): 1869 - 1886. [Abstract] [Full Text] [PDF]
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T. Hadrys, R. DeSalle, S. Sagasser, N. Fischer, and B. Schierwater The Trichoplax PaxB Gene: A Putative Proto-PaxA/B/C Gene Predating the Origin of Nerve and Sensory Cells Mol. Biol. Evol., July 1, 2005; 22(7): 1569 - 1578. [Abstract] [Full Text] [PDF]
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P. Zhang, H. Zhou, Y.-Q. Chen, Y.-F. Liu, and L.-H. Qu Mitogenomic Perspectives on the Origin and Phylogeny of Living Amphibians Syst Biol, June 1, 2005; 54(3): 391 - 400. [Abstract] [Full Text] [PDF]
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H. S. Yoon, J. D. Hackett, F. M. Van Dolah, T. Nosenko, K. L. Lidie, and D. Bhattacharya Tertiary Endosymbiosis Driven Genome Evolution in Dinoflagellate Algae Mol. Biol. Evol., May 1, 2005; 22(5): 1299 - 1308. [Abstract] [Full Text] [PDF]
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N. Iwabe, Y. Hara, Y. Kumazawa, K. Shibamoto, Y. Saito, T. Miyata, and K. Katoh Sister Group Relationship of Turtles to the Bird-Crocodilian Clade Revealed by Nuclear DNA-Coded Proteins Mol. Biol. Evol., April 1, 2005; 22(4): 810 - 813. [Abstract] [Full Text] [PDF]
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T.-K. Seo, H. Kishino, and J. L. Thorne Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data PNAS, March 22, 2005; 102(12): 4436 - 4441. [Abstract] [Full Text] [PDF]
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