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Group: FAB-lab - with tag methods [141 articles]

Recent papers posted by members of the FAB-lab group with tag methods
  • Mixture models in phylogenetic inference
    (28 April 2008)
    by Mark Pagel
    posted to bayesian markov-chains methods monte-carlo phylogeny rates substitution-models by rvosa to the group FAB-lab on 2008-08-18 02:27:00 as **
  • Modelling Heterotachy in Phylogenetic Inference by Reversible-Jump Markov chain Monte Carlo
    Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, Vol. In review
    by Mark Pagel, Andrew Meade
    posted to bayesian markov-chains methods monte-carlo rates substitution-models by rvosa to the group FAB-lab on 2008-08-18 01:50:23 as **
  • Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data.
    Computer Appl. Biosciences, Vol. 11 (1999), pp. 247-251.
    by Andy Purvis, Andrew Rambaut
    posted to comparative methods software by rvosa to the group FAB-lab on 2008-08-14 03:02:20 as **
  • Use and misuse of the gene ontology annotations.
    Nature reviews. Genetics (13 May 2008)
    by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici
    posted to genetics genome methods ontology programming by rvosa to the group FAB-lab on 2008-08-12 07:52:51 as ** along with 21 people and 1 group jfr djkt jyuh aheilbut mariakmejia cmzmasek A_Olympia realzhang carlk roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck bpcusack logics of knowledge
  • Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
    Systematic Zoology, Vol. 27, No. 4. (1978), pp. 401-410.
    by Joseph Felsenstein
    posted to characters inference methods parsimony phylogeny by rvosa to the group FAB-lab on 2008-08-12 05:17:15 as **
  • Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models
    Mol Biol Evol, Vol. 21, No. 7. (1 July 2004), pp. 1332-1339.
    by Jianzhi Zhang
    posted to genetics likelihood methods selection sequence-evolution substitution-models by rvosa to the group FAB-lab on 2008-08-12 04:02:24 as ** along with 1 person Garamonfok
  • Calculating independent contrasts for the comparative study of substitution rates.
    Journal of theoretical biology, Vol. 251, No. 4. (21 April 2008), pp. 667-678.
    by JJ Welch, D Waxman
    posted to comparative contrasts likelihood methods rates substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:42:43 as **
  • Phylogenetic Mixture Models Can Reduce Node-Density Artifacts
    Systematic Biology, Vol. 57, No. 2. (2008), pp. 286-293.
    by Chris Venditti, Andrew Meade, Mark Pagel
    posted to inference methods models phylogeny sequence-evolution substitution-models by rvosa to the group FAB-lab on 2008-08-09 10:43:23 as ** along with 1 person aprasad
  • A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data
    Systematic Biology, Vol. 53, No. 4., 571.
    by Mark Pagel, Andrew Meade
    posted to characters genetics methods models phylogeny sequence substitution-models by rvosa to the group FAB-lab on 2008-08-09 10:21:04 as ** along with 1 person taka
  • Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible-Jump Markov Chain Monte Carlo.
    The American naturalist, Vol. 167, No. 6. (9 May 2006)
    by Mark Pagel, Andrew Meade
    posted to bayesian characters comparative evolution markov-chains methods monte-carlo statistics by rvosa to the group FAB-lab on 2008-08-09 09:41:27 as **
  • BranchClust: A phylogenetic algorithm for selecting gene families
    BMC Bioinformatics, Vol. 8 (10 April 2007), 120.
    by Maria S Poptsova, Peter J Gogarten
    posted to algorithms alignment data-mining genome homology methods phylogenomics phyloinformatics programming by rvosa to the group FAB-lab on 2008-08-08 07:02:46 as ** along with 2 people and 1 group dandaman stajich Berkeley Mycology
  • 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 bacteria comparative divergence fungi methods rates ratio-test substitution-models 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 algorithms bayesian markov-chains methods monte-carlo statistics by rvosa to the group FAB-lab on 2008-05-13 01:30:09 as ** along with 12 people and 1 group okouma ldietz pcarbo icosma adriandefroment leonnovelo i-stevenson jrw quianominorleo ansobol markusd nojhan Metaheuristics
  • What is principal component analysis?
    Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.
    by Markus Ringnér
    posted to data-mining methods statistics by rvosa to the group FAB-lab on 2008-05-13 01:28:59 as ** along with 54 people and 2 groups Yanno jyuh operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu rsantana laharrin sobolevnrm fryanpan kengg dekay23 adacier hpaces waghsk rchauhan pavanghatty kristgy jfr bibay2004 xingxu quianominorleo abbie_riner craigwilson06 ashko markusd dayjm dimka i-stevenson chrissp100 tharris ale mjoach HugoMarcelo jdiezperezj rrbarb Nici baker-group Bioinformatics
  • 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 along with 1 person jandot
  • 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 **
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