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Group: FAB-lab - with tag algorithms [45 articles]

Recent papers posted by members of the FAB-lab group with tag algorithms
  • 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
  • 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
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • notes NJML: A hybrid algorithm for the neighbor-joining and maximum-likelihood methods
    Molecular Biology and Evolution, Vol. 17, No. 9. (2000), pp. 1401-1409.
    by S Ota, WH Li
    posted to algorithms bibtex-import likelihood phenetics 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 **
  • Dictionary of Algorithms and Data Structures
    (August August, February00May 2005)
    by T Nis
    posted to algorithms bibtex-import programming by rvosa to the group FAB-lab on 2008-02-06 23:58:18 as **
  • Simulated evolutionary optimization and local search: Introduction and application to tree search
    Cladistics, Vol. 17, No. 1. (2001), pp. S12-S25.
    by A Moilanen
    posted to algorithms bibtex-import methods phylogeny simulation by rvosa to the group FAB-lab on 2008-02-06 23:58:18 as **
  • Assessing progress in systematics with continuous jackknife function analysis
    Systematic Biology, Vol. 52, No. 1. (2003), pp. 55-65.
    by JA Miller
    posted to algorithms bibtex-import characters methods phylogeny weighting by rvosa to the group FAB-lab on 2008-02-06 23:58:17 as **
  • Equations of state calculations by fast computing machines
    J. Chem. Phys., Vol. 21 (1953), pp. 1087-1091.
    by N Metropolis, AW Rosenbluth, MN Rosenbluth, AH Teller, E Teller
    posted to algorithms bibtex-import programming by rvosa to the group FAB-lab on 2008-02-06 23:58:17 as **
  • notes A Genetic Algorithm for Maximum-Likelihood Phylogeny Inference Using Nucleotide Sequence Data
    Molecular Biology and Evolution, Vol. 15, No. 3. (1998), pp. 277-283.
    by Paul O Lewis
    posted to algorithms bibtex-import inference likelihood methods phylogeny reconstruction by rvosa to the group FAB-lab on 2008-02-06 23:58:15 as **
  • notes Markov Chain Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees
    Molecular Biology and Evolution, Vol. 16, No. 6. (1999), pp. 750-759.
    by Bret Larget, Donald L Simon
    posted to algorithms bayesian bibtex-import markov-chains methods monte-carlo phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:15 as **
  • Quantitative phyletics and the evolution of anurans
    Systematic Zoology, Vol. 40 (1969), pp. 446-457.
    by AG Kluge, James S Farris
    posted to algorithms bibtex-import characters methods by rvosa to the group FAB-lab on 2008-02-06 23:58:15 as **
  • Homoplasy Increases Phylogenetic Structure
    Cladistics, Vol. 15 (1999), pp. 91-93.
    by Mari Kallersjo, Victor A Albert, James S Farris
    posted to algorithms bibtex-import methods parsimony by rvosa to the group FAB-lab on 2008-02-06 23:58:14 as **
  • Bonsai: teaching a clown to prune trees
    No. CMPT TR 91-6. (1991)
    by L Hafer
    posted to algorithms bibtex-import programming topology by rvosa to the group FAB-lab on 2008-02-06 23:58:10 as **
  • Analyzing large data sets in reasonable times: Solutions for composite optima
    Cladistics, Vol. 15, No. 4. (1999), pp. 415-428.
    by PA Goloboff
    posted to algorithms bibtex-import methods parsimony phyloinformatics by rvosa to the group FAB-lab on 2008-02-06 23:58:09 as **
  • The agreement metric for labeled binary trees
    Mathematical Bioscience, Vol. 123 (1994), pp. 215-226.
    by W Goddard, E Kubicka, G Kubicki, FR Mcmorris
    posted to algorithms bibtex-import methods phylogeny topology by rvosa to the group FAB-lab on 2008-02-06 23:58:09 as **
  • notes Inferring phylogenies from DNA sequences of unequal base compositions
    Proceedings of the National Academy of Sciences USA, Vol. 92 (1995), pp. 11317-11321.
    by Nicolas Galtier, Manolo Gouy
    posted to algorithms bibtex-import genetics markov-chains methods monte-carlo phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:08 as **
  • Confidence limits on phylogenies: an approach using the bootstrap
    Evolution, Vol. 39 (1985), pp. 783-791.
    by Joseph Felsenstein
    posted to algorithms bibtex-import methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:07 as **
  • The retention index and the rescaled consistency index
    Cladistics, Vol. 5 (1989), pp. 417-419.
    by James S Farris
    posted to algorithms bibtex-import characters methods phylogeny topology by rvosa to the group FAB-lab on 2008-02-06 23:58:07 as **
  • Graph Theory
    Vol. 173 (2005)
    by Reinhard Diestel
    posted to algorithms bibtex-import graph networks topology by rvosa to the group FAB-lab on 2008-02-06 23:58:07 as **
  • Toward a characterization of landscapes of combinatorial optimization problems, with special attention to the phylogeny problem
    Journal of Computational Biology, Vol. 2, No. 3. (1995), pp. 439-450.
    by MA Charleston
    posted to algorithms bibtex-import methods phylogeny by rvosa to the group FAB-lab on 2008-02-06 23:58:04 as **
  • A method for deducing branching sequences in phylogeny
    Evolution, Vol. 19 (1965), pp. 311-326.
    by JH Camin, RR Sokal
    posted to algorithms bibtex-import methods phylogeny topology by rvosa to the group FAB-lab on 2008-02-06 23:58:03 as **
  • Branch support and tree stability
    Cladistics, Vol. 10 (1994), pp. 295-304.
    by K Bremer
    posted to algorithms bibtex-import methods topology by rvosa to the group FAB-lab on 2008-02-06 23:58:03 as **
  • Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
    Taxon, Vol. 41 (1992), pp. 3-10.
    by BR Baum
    posted to algorithms bibtex-import data-mining methods mrp phyloinformatics supertree by rvosa to the group FAB-lab on 2008-02-06 23:58:02 as **
  • Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom
    BMC Evolutionary Biology, Vol. 7 (09 August 2007), 134.
    by Eiko E Kuramae, Vincent Robert, Carlos Echavarri-Erasun, Teun Boekhout
    posted to algorithms amino-acid data-mining fungi methods phylogenomics phylogeny phyloinformatics proteins by rvosa to the group FAB-lab on 2008-02-01 11:30:06 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to algorithms alignment methods sequence by rvosa to the group FAB-lab on 2008-02-01 11:26:13 as ** along with 10 people and 1 group mdimmic timflutre stajich zwang cabbagezs groepl yoanjacquemin marti smbe2008 giovenko Bioinformatics
  • Profiling Phylogenetic Informativeness
    Systematic Biology, Vol. 56, No. 2. (2007), pp. 222-231.
    by Jeffrey P Townsend
    posted to algorithms animals characters data-mining mammal mammals methods mice phylogeny phyloinformatics rodents vertebrates by rvosa to the group FAB-lab on 2008-02-01 11:18:23 as ** along with 3 people and 1 group aprasad stajich Jporci Berkeley Mycology
  • Improved Consensus Network Techniques for Genome-Scale Phylogeny
    Molecular Biology and Evolution, Vol. 23, No. 5. (15 May 2006), pp. 848-855.
    by Barbara R Holland, Lars S Jermiin, Vincent Moulton
    posted to algorithms genome graph methods networks phylogenomics phylogeny phyloinformatics by rvosa to the group FAB-lab on 2008-02-01 11:14:28 as ** along with 1 person stajich
  • Detecting and overcoming systematic errors in genome-scale phylogenies.
    Syst Biol, Vol. 56, No. 3. (June 2007), pp. 389-399.
    by N Rodríguez-Ezpeleta, H Brinkmann, B Roure, N Lartillot, BF Lang, H Philippe
    posted to algorithms databases data-mining genome methods phylogenomics phylogeny phyloinformatics by rvosa to the group FAB-lab on 2008-02-01 11:12:39 as ** along with 3 people and 1 group aprasad stajich dandaman Berkeley Mycology
  • New Approaches to Phylogenetic Tree Search and Their Application to Large Numbers of Protein Alignments
    Systematic Biology, Vol. 56, No. 5. (2007), pp. 727-740.
    by Simon Whelan
    posted to algorithms amino-acid methods phylogeny proteins software by rvosa to the group FAB-lab on 2008-02-01 11:11:01 as ** along with 1 person stajich
  • The Bioperl Toolkit: Perl Modules for the Life Sciences
    Genome Res., Vol. 12, No. 10. (1 October 2002), pp. 1611-1618.
    by Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson, Ewan Birney
    posted to algorithms alignment databases data-mining methods programming software by rvosa to the group FAB-lab on 2008-02-01 11:05:23 as ** along with 17 people and 1 group jmeppley chad_davis indigoviolet skhadar dullhunk dgront stajich noby incovoma glycine tyrosine threonine valine nklee hpaces sekmi ninch EisenLab
  • Distinguishing protein-coding and noncoding genes in the human genome
    Proceedings of the National Academy of Sciences (26 November 2007), 0709013104.
    by Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S Lander
    posted to algorithms amino-acid animals data-mining genetics genome hominidae homology humans mammals methods phylogenomics primates proteins rna sequence vertebrates by rvosa to the group FAB-lab on 2008-02-01 11:04:06 as ** along with 15 people and 2 groups tmmurali balicea sebastien_vigneau giovanni neils stajich cjeans cabbagezs maximilianh oelemento gjuggler slroberd renatomilani gracio Ema EisenLab Berkeley Mycology
  • Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments
    Mol Biol Evol, Vol. 24, No. 6. (1 June 2007), pp. 1380-1383.
    by Giddy Landan, Dan Graur
    posted to algorithms alignment amino-acid data-mining dna methods phylogeny phyloinformatics sequence by rvosa to the group FAB-lab on 2008-02-01 11:01:06 as ** along with 7 people aprasad BioNica stajich cjeans zwang lilou mailund
  • Assessing performance of orthology detection strategies applied to eukaryotic genomes.
    PLoS ONE, Vol. 2 (2007)
    by F Chen, AJ Mackey, JK Vermunt, DS Roos
    posted to algorithms databases data-mining genome methods phylogenomics phylogeny phyloinformatics by rvosa to the group FAB-lab on 2008-02-01 10:57:03 as ** along with 10 people and 2 groups druvus icases operon indigoviolet stajich cjeans winterschlaefer bpcusack cerca natstreet EisenLab TNT
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