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Group: FAB-lab - with tag methods [130 articles]

Recent papers posted by members of the FAB-lab group with tag methods
  • Accelerated molecular evolution as a consequence of transitions to mutualism
    Proceedings of the national academy of sciences, Vol. 94, No. 21. (1997), pp. 11422-11427.
    by Francois Lutzoni, Mark Pagel
    posted to substitution-models ratio-test rates methods fungi divergence comparative bacteria by rvosa to the group FAB-lab on 2008-07-11 18:54:57 as **
  • Understanding the Metropolis-Hastings Algorithm
    The American Statistician, Vol. 49, No. 4. (1995), pp. 327-335.
    by Siddhartha Chib, Edward Greenberg
    posted to statistics monte-carlo methods markov-chains bayesian algorithms by rvosa to the group FAB-lab on 2008-05-13 01:30:09 as ** along with 11 people and 1 group i-stevenson ansobol quianominorleo jrw nojhan markusd ldietz pcarbo icosma adriandefroment leonnovelo Metaheuristics
  • What is principal component analysis?
    Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.
    by Markus Ringnér
    posted to statistics methods data-mining by rvosa to the group FAB-lab on 2008-05-13 01:28:59 as ** along with 52 people and 2 groups mjoach ale rrbarb HugoMarcelo tharris rsantana kengg laharrin chrissp100 xingxu dekay23 i-stevenson dimka dayjm markusd ashko craigwilson06 abbie_riner quianominorleo bibay2004 jfr kristgy pavanghatty rchauhan waghsk hpaces adacier fryanpan sobolevnrm Yanno jyuh operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu Bioinformatics baker-group
  • Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).
    Omics : a journal of integrative biology, Vol. 10, No. 2. (2006), pp. 231-237.
    by J Leebens-Mack, T Vision, E Brenner, JE Bowers, S Cannon, MJ Clement, CW Cunningham, C dePamphilis, R deSalle, JJ Doyle, JA Eisen, X Gu, J Harshman, RK Jansen, EA Kellogg, EV Koonin, BD Mishler, H Philippe, JC Pires, YL Qiu, SY Rhee, K Sjölander, DE Soltis, PS Soltis, DW Stevenson, K Wall, T Warnow, C Zmasek
    posted to methods by rvosa to the group FAB-lab on 2008-04-22 20:26:55 as read
  • Missing data, incomplete taxa, and phylogenetic accuracy
    Systematic Biology, Vol. 52, No. 4. (2003), pp. 528-538.
    by JJ Wiens
    posted to bibtex-import characters data-mining fossils methods parsimony phylogeny phyloinformatics simulation by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • A novel method for economical diagnosis of cladograms under Sankoff optimization
    Cladistics, Vol. 10 (1994), pp. 207-213.
    by Ward C Wheeler, Kevin Nixon
    posted to algorithms bibtex-import methods parsimony phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • Iterative pass optimization of sequence data
    Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 3. (2003), pp. 254-260.
    by WC Wheeler
    posted to algorithms alignment bibtex-import methods phylogeny sequence by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • Search-based optimization
    Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 4. (2003), pp. 348-355.
    by WC Wheeler
    posted to alignment bibtex-import methods parsimony by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure
    Cladistics, Vol. 6 (1990), pp. 269-275.
    by Ward C Wheeler
    posted to algorithms bibtex-import methods parsimony phylogeny weighting by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • Noise
    Cladistics, Vol. 15 (1999), pp. 51-64.
    by John W Wenzel, Mark E Siddall
    posted to bibtex-import methods parsimony phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:30 as **
  • notes IQPNNI: Moving Fast Through Tree Space and Stopping in Time
    Molecular Biology and Evolution, Vol. 21, No. 8. (2004), pp. 1565-1571.
    by Le S Vinh, Arndt von Haeseler
    posted to algorithms bibtex-import likelihood methods by rvosa to the group FAB-lab on 2008-02-06 23:58:29 as **
  • notes Inching toward Reality: An Improved Likelihood Model of Sequence Evolution
    Journal of Molecular Evolution, Vol. 34 (1992), pp. 3-16.
    by Jeffrey L Thorne, Hirohisa Kishino, Joseph Felsenstein
    posted to algorithms alignment bibtex-import evolution likelihood methods programming substitution-models by rvosa to the group FAB-lab on 2008-02-06 23:58:28 as **
  • Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used
    Molecular Biology and Evolution, Vol. 17, No. 8. (2000), pp. 1251-1258.
    by K Takahashi, M Nei
    posted to algorithms bibtex-import likelihood methods parsimony by rvosa to the group FAB-lab on 2008-02-06 23:58:28 as **
  • Global lability, regional resolution, and majority-rule consensus bias
    Paleobiology, Vol. 27, No. 2. (2001), pp. 254-261.
    by CD Sumrall, CA Brochu, JW Merck
    posted to bibtex-import fossils methods by rvosa to the group FAB-lab on 2008-02-06 23:58:28 as **
  • Distributions of Tree Comparison Metrics - Some New Results
    Systematic Biology, Vol. 42, No. 2. (1993), pp. 126-141.
    by MA Steel, D Penny
    posted to algorithms bibtex-import evolution methods phylogeny topology by rvosa to the group FAB-lab on 2008-02-06 23:58:27 as **
  • The maximum likelihood point for a phylogenetic tree is not unique
    Systematic Biology, Vol. 43 (1994), pp. 560-564.
    by MA Steel
    posted to bibtex-import likelihood methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:27 as **
  • Numerical taxonomy: The principles and practice of numerical classification.
    (1973)
    by PHA Sneath, RR Sokal
    posted to bibtex-import classification methods phylogeny taxonomy by rvosa to the group FAB-lab on 2008-02-06 23:58:27 as **
  • Amino acid vs. nucleotide characters: challenging preconceived notions
    Molecular Phylogenetics and Evolution, Vol. 24 (2002), pp. 78-90.
    by MP Simmons, H Ochoterena, JV Freudenstein
    posted to amino-acid bibtex-import characters dna methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:26 as **
  • PAUPRat: PAUP* implementation of the parsimony ratchet.
    (2001)
    by DS Sikes, Paul O Lewis
    posted to algorithms bibtex-import methods parsimony software by rvosa to the group FAB-lab on 2008-02-06 23:58:26 as **
  • Brooks parsimony analysis: a valiant failure
    Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 6. (2003), pp. 554-564.
    by ME Siddall, SL Perkins
    posted to bibtex-import methods parsimony by rvosa to the group FAB-lab on 2008-02-06 23:58:26 as **
  • A hypothesis-independent method of character weighting for cladistic analysis
    Cladistics, Vol. 5 (1989), pp. 63-86.
    by Michael J Sharkey
    posted to bibtex-import characters methods parsimony phylogeny weighting by rvosa to the group FAB-lab on 2008-02-06 23:58:26 as **
  • Supertree algorithms for ancestral divergence dates and nested taxa
    Bioinformatics, Vol. 20, No. 0. (2004), pp. 1-6.
    by C Semple, P Daniel, W Hordijk, Page, MA Steel
    posted to algorithms bibtex-import divergence methods phylogeny supertree by rvosa to the group FAB-lab on 2008-02-06 23:58:26 as **
  • Simultaneous analysis of basal Hymenoptera (Insecta): introducing robust-choice sensitivity analysis
    Biological Journal of the Linnean Society, Vol. 79, No. 2. (2003), pp. 245-275.
    by S Schulmeister
    posted to animals bibtex-import classification insects invertebrates methods phylogeny taxonomy by rvosa to the group FAB-lab on 2008-02-06 23:58:25 as **
  • Review of morphological evidence on the phylogeny of basal Hymenoptera (Insecta), with a discussion of the ordering of characters
    Biological Journal of the Linnean Society, Vol. 79, No. 2. (2003), pp. 209-243.
    by S Schulmeister
    posted to animals bibtex-import characters data-mining insects invertebrates methods morphology phylogeny phyloinformatics by rvosa to the group FAB-lab on 2008-02-06 23:58:25 as **
  • notes Phylogenetic supertrees: assembling the trees of life
    Trends in Ecology and Evolution, Vol. 13, No. 3. (1998), pp. 105-109.
    by Michael J Sanderson, Andy Purvis, Chris Henze
    posted to bibtex-import methods mrp phylogeny supertree by rvosa to the group FAB-lab on 2008-02-06 23:58:24 as **
  • Stochastic search strategy for estimation of maximum likelihood phylogenetic trees
    Systematic Biology, Vol. 50, No. 1. (2001), pp. 7-17.
    by LA Salter, DK Pearl
    posted to bibtex-import likelihood methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:24 as **
  • Complexity of the likelihood surface for a large DNA dataset
    Systematic Biology, Vol. 50, No. 6. (2001), pp. 970-978.
    by LA Salter
    posted to bibtex-import likelihood methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:24 as **
  • notes Building Supertrees: an Empirical Assessment using the Grass Family (Poaceae)
    Systematic Biology, Vol. 51, No. 1. (2002), pp. 136-150.
    by N Salamin, TR Hodkinson, V Savolainen
    posted to bibtex-import methods mrp phylogeny plants supertree by rvosa to the group FAB-lab on 2008-02-06 23:58:24 as **
  • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    Molecular Biology and Evolution, Vol. 4 (1987), pp. 406-425.
    by N Saitou, M Nei
    posted to algorithms bibtex-import methods phenetics phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:24 as **
  • Taxon sampling, bioinformatics, and phylogenomics
    Systematic Biology, Vol. 52, No. 1. (2003), pp. 119-124.
    by MS Rosenberg, S Kumar
    posted to bibtex-import methods phylogenomics phyloinformatics by rvosa to the group FAB-lab on 2008-02-06 23:58:23 as **
  • Bayesian supertrees
    (2004)
    by F Ronquist, John P Huelsenbeck, T Britton
    edited by Olaf
    posted to bayesian bibtex-import methods supertree by rvosa to the group FAB-lab on 2008-02-06 23:58:23 as **
  • notes Matrix representation of trees, redundancy, and weighting
    Systematic Biology, Vol. 45 (1996), pp. 251-255.
    by F Ronquist
    posted to bibtex-import methods mrp supertree weighting by rvosa to the group FAB-lab on 2008-02-06 23:58:23 as **
  • Multiple local maxima for likelihoods of phylogenetic trees: a simulation study.
    Molecular Biology and Evolution, Vol. 16 (1999), pp. 1079-1085.
    by J Rogers, DL Swofford
    posted to bibtex-import likelihood methods phylogeny simulation by rvosa to the group FAB-lab on 2008-02-06 23:58:23 as **
  • Cladistic analysis of languages: Indo-European classification based on lexicostatistical data
    Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 2. (2003), pp. 120-127.
    by K Rexova, D Frynta, J Zrzavy
    posted to bibtex-import classification lexicostatistics methods by rvosa to the group FAB-lab on 2008-02-06 23:58:23 as **
  • notes Estimating divergence dates from molecular sequences
    Molecular Biology and Evolution, Vol. 15, No. 4. (1998), pp. 442-448.
    by A Rambaut, L Bromham
    posted to animals bibtex-import birds clock-like divergence dna evolution fossils likelihood mammals methods mitochondrial phylogeny rates sequence substitution-models vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:22 as **
  • Phylogenetic inference based on matrix representation of trees
    Molecular Phylogenetics and Evolution, Vol. 1 (1992), pp. 53-58.
    by MA Ragan
    posted to bibtex-import methods mrp phylogeny supertree by rvosa to the group FAB-lab on 2008-02-06 23:58:22 as **
  • An integrated framework for the inference of viral population history from reconstructed genealogies
    Genetics, Vol. 155 (2000), pp. 1429-1437.
    by OG Pybus, A Rambaut, PH Harvey
    posted to bibtex-import diversification methods phylogeny population-genetics viruses by rvosa to the group FAB-lab on 2008-02-06 23:58:21 as **
  • Building phylogenies: are the big easy?
    Trends in Ecology and Evolution, Vol. 12, No. 2. (1997)
    by Andy Purvis, Donald LJ Quicke
    posted to bibtex-import methods phylogeny phyloinformatics by rvosa to the group FAB-lab on 2008-02-06 23:58:21 as **
  • notes A modification to Baum and Ragan's method for combining phylogenetic trees
    Systematic Biology, Vol. 44, No. 2. (1995), pp. 251-255.
    by Andy Purvis
    posted to bibtex-import methods mrp phyloinformatics supertree weighting by rvosa to the group FAB-lab on 2008-02-06 23:58:21 as **
  • Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods
    Systematic Biology, Vol. 52, No. 3. (2003), pp. 423-428.
    by S Poe
    posted to bibtex-import methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:21 as **
  • History influences signal recognition: neural network models of tungara frogs
    Proceedings of the Royal Society London Series B, Vol. 267 (2000), pp. 1633-1639.
    by SM Phelps, MJ Ryan
    posted to animals behaviour bibtex-import methods phylogeny selection sexual vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:21 as **
  • The use of tree comparison metrics
    Systematic Zoology, Vol. 34 (1985), pp. 75-82.
    by D Penny, MP Hendy
    posted to algorithms bibtex-import methods topology by rvosa to the group FAB-lab on 2008-02-06 23:58:21 as **
  • Analyses of Phylogenetics and Evolution: the ape Package
    (2003)
    by E Paradis, Korbinian Strimmer, J Claude, Y Noel, B Bolker
    posted to bibtex-import diversification methods models programming rates reconstruction software topology by rvosa to the group FAB-lab on 2008-02-06 23:58:19 as **
  • notes Inferring evolutionary processes from phylogenies
    Zoologica Scripta, Vol. 26, No. 4. (1997), pp. 331-348.
    by M Pagel
    posted to animals bibtex-import diversification evolution extinction inference methods models primates reconstruction vertebrates by rvosa to the group FAB-lab on 2008-02-06 23:58:19 as **
  • Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters
    Proceedings of the Royal Society London Series B, Vol. 255 (1994), pp. 37-45.
    by M Pagel
    posted to bibtex-import characters comparative evolution likelihood methods phylogeny reconstruction by rvosa to the group FAB-lab on 2008-02-06 23:58:19 as **
  • From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem
    Molecular Phylogenetics and Evolution, Vol. 7, No. 2. (1997), pp. 231-240.
    by Page, MA Charleston
    posted to bibtex-import classification genetics methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:19 as **
  • On islands of trees and the efficacy of different methods of branch-swapping in finding most parsimonious trees
    Systematic Biology, Vol. 42, No. 200-210. (1993)
    by Page
    posted to bibtex-import methods parsimony by rvosa to the group FAB-lab on 2008-02-06 23:58:19 as **
  • notes NJML+: An extension of the NJML method to handle protein sequence data and computer software implementation
    Molecular Biology and Evolution, Vol. 18, No. 11. (2001), pp. 1983-1992.
    by S Ota, WH Li
    posted to algorithms amino-acid bibtex-import likelihood methods phenetics protein software by rvosa to the group FAB-lab on 2008-02-06 23:58:19 as **
  • The problem with the Paleoptera Problem: sense and sensitivity
    Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 5. (2003), pp. 432-442.
    by TH Ogden, MF Whiting
    posted to alignment animals bibtex-import classification diversification dna insects invertebrates methods morphology phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:18 as **
  • The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
    Cladistics, Vol. 15 (1999), pp. 407-414.
    by Kevin Nixon
    posted to algorithms bibtex-import methods parsimony phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:18 as **
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