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Tag phylogeny [703 articles]

Recent papers classified by the tag phylogeny.
  • Non-random coextinctions in phylogenetically structured mutualistic networks
    Nature, Vol. 448, No. 7156., pp. 925-928.
    by Enrico L Rezende, Jessica E Lavabre, Paulo R Guimarães, Pedro Jordano, Jordi Bascompte
    posted to co-extinction mutation network phylogeny by zwang on 2007-08-28 04:03:13 as *** along with 1 person cmm
  • New Taxonomy and the Origin of Species
    PLoS Biology, Vol. 5, No. 7. (1 July 2007), e194.
    by Shai Meiri, Georgina M Mace
    posted to evolution phylogeny specy by zwang on 2007-08-29 02:19:57 as ** along with 1 person asddd
  • The prokaryotic tree of life: past, present...and future?
    Trends in Ecology & Evolution, Vol. 23, No. 5. (May 2008), pp. 276-281.
    by James O Mcinerney, James A Cotton, Davide Pisani
    posted to evolution phylogeny prokaryote by zwang on 2008-06-16 01:48:25 as ** along with 2 people and 2 groups balicea jlgreen Green Lab iSEEM
  • Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans
    Current Biology, Vol. 17, No. 16. (21 August 2007), pp. 1420-1425.
    by Naiara Rodriguez-Ezpeleta, Henner Brinkmann, Gertraud Burger, Andrew J Roger, Michael W Gray, Herve Philippe, Franz B Lang
    posted to eukaryota evolution phylogeny specy by zwang on 2007-08-28 04:01:45 as ** along with 1 person asddd
  • Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph
    PLoS Genet, Vol. 4, No. 10. (10 October 2008), e1000212.
    by Yonghui Wu, Prasanna R Bhat, Timothy J Close, Stefano Lonardi
    posted to phylogeny evolution by zwang on 2008-11-03 10:12:51 as *** along with 2 people djkt Ema
  • Constraint-based functional similarity of metabolic genes: going beyond network topology
    Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2139-2146.
    by Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y Pinter
    posted to gene network phylogeny by zwang on 2007-09-17 09:39:55 as *** along with 1 person ptrobajo
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to alignment evolution phylogeny by zwang on 2008-06-25 05:44:44 as *** along with 23 people and 3 groups pradiptaray alexeid marti bpcusack hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology aprasad bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
  • SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e149.
    by Irmtraud M Meyer, István Miklós
    posted to alignment bayesian phylogeny rna structure by zwang on 2007-09-13 17:47:28 as **** along with 3 people raylim cabbagezs bertelsen
  • Probabilistic Phylogenetic Inference with Insertions and Deletions
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000172.
    by Elena Rivas, Sean R Eddy
    posted to phylogeny evolution by zwang on 2008-10-20 01:59:53 as **** along with 9 people and 1 group treangen pradiptaray nuin timflutre druvus djkt aprasad gjuggler emptyhb iSEEM
  • A Comprehensive Phylogeny of Beetles Reveals the Evolutionary Origins of a Superradiation
    Science, Vol. 318, No. 5858. (21 December 2007), pp. 1913-1916.
    by Toby Hunt, Johannes Bergsten, Zuzana Levkanicova, Anna Papadopoulou, Oliver S John, Ruth Wild, Peter M Hammond, Dirk Ahrens, Michael Balke, Michael S Caterino, Jesus Gomez-Zurita, Ignacio Ribera, Timothy G Barraclough, Milada Bocakova, Ladislav Bocak, Alfried P Vogler
    posted to evolution phylogeny by zwang on 2007-12-21 09:47:02 as *** along with 2 people dinnes youdon
  • Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution
    BMC Evolutionary Biology, Vol. 7 (16 May 2007), 78.
    by Chrstian Rausch, Ilka Hoof, Tilmann Weber, Wolfgang Wohlleben, Daniel H Huson
    posted to domain evolution phylogeny by zwang on 2007-06-14 02:21:21 as ** along with 1 person pradiptaray
  • Using Phylogeny to Improve Genome-Wide Distant Homology Recognition
    PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e3.
    by Sanne Abeln, Carlo Teubner, Charlotte M Deane
    posted to genome-wide homology phylogeny by zwang on 2007-04-12 10:35:42 as ****
  • High-resolution species trees without concatenation
    PNAS, Vol. 104, No. 14. (3 April 2007), pp. 5936-5941.
    by Scott V Edwards, Liang Liu, Dennis K Pearl
    posted to phylogeny specy by zwang on 2007-04-06 05:45:14 as ** along with 6 people and 1 group treangen druvus alexeid stevanspringer operon aprasad FAB-lab
  • Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e51.
    by Barry G Hall, Stephen J Salipante
    posted to accuracy clade confidence phylogeny by zwang on 2007-04-02 09:10:51 as *** along with 1 person operon
  • Phylogenetic exploration of bacterial genomic rearrangements
    Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1172-1174.
    by Romain Fremez, Thomas Faraut, Gwennaele Fichant, Jerome Gouzy, Yves Quentin
    posted to bacterial genome phylogeny by zwang on 2007-05-10 08:13:26 as ** along with 3 people druvus treangen operon
  • Phylogenetic Methodology for Detecting Protein Interactions
    Mol Biol Evol, Vol. 24, No. 3. (1 March 2007), pp. 650-659.
    by Peter J Waddell, Hirohisa Kishino, Rissa Ota
    posted to interaction phylogeny protein by zwang on 2007-03-30 08:51:26 as *** along with 2 people and 1 group stevanspringer tale FAB-lab
  • Phylogenetic Inference Using Whole Genomes
    Annual Review of Genomics and Human Genetics, Vol. 9, No. 1. (2008), pp. 217-231.
    by Bruce Rannala, Ziheng Yang
    posted to phylogeny genome by zwang on 2008-09-04 06:33:51 as ** along with 4 people treangen druvus aprasad gjuggler
  • A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution
    Mol Biol Evol, Vol. 23, No. 9. (1 September 2006), pp. 1724-1730.
    by Beth Shapiro, Andrew Rambaut, Oliver G Pybus, Edward C Holmes
    posted to evolution phylogeny positiveepistasis by zwang on 2007-04-16 14:16:08 as * along with 1 person and 1 group stevanspringer FAB-lab
  • Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes
    Nucl. Acids Res., Vol. 35, No. 7. (1 April 2007), pp. 2283-2294.
    by Yanglong Zhu, Dileep K Pulukkunat, Yong Li
    posted to diversity phylogeny rna structure by zwang on 2007-05-08 12:14:37 as ***
  • Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data
    Mol Biol Evol, Vol. 25, No. 5. (1 May 2008), pp. 960-971.
    by Tae-Kun Seo
    posted to bootstrap evolution phylogeny sequence by zwang on 2008-04-15 05:10:40 as ** along with 1 person adacier
  • Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e237.
    by Juan A Ranea, Corin Yeats, Alastair Grant, Christine A Orengo
    posted to eukaryota genome hierarchical phylogeny prediction protein by zwang on 2007-12-10 04:43:48 as *** along with 5 people marti eckart_bindewald skhadar asddd hpaces
  • Phylogenetic Approaches to the Study of Extinction
    Annual Review of Ecology, Evolution, and Systematics, Vol. 39, No. 1. (2008), pp. 301-319.
    by Andy Purvis
    posted to phylogeny evolution by zwang on 2008-11-04 04:11:40 as **
  • Evolution of genes and genomes on the Drosophila phylogeny
    Nature, Vol. 450, No. 7167. (November 2007), pp. 203-218.
    posted to evolution gene genome phylogeny by zwang on 2007-11-20 09:04:25 as **** along with 23 people and 6 groups jbsaltz druvus pradiptaray pengchy operon tmmurali indigoviolet djkt timflutre stajich Garamonfok lp2 CharlesM hpaces caseybrown emptyhb urgi noor PetrovLab isimpson balicea cisevol hdopazo Bioinformatics EisenLab csb_journal_club_public Berkeley Mycology BergmanLab Drosophila-Genetics-Genomics-2008
  • Global molecular phylogeography reveals persistent Arctic circumpolar isolation in a marine planktonic protist
    PNAS, Vol. 104, No. 12. (20 March 2007), pp. 5002-5007.
    by Kate F Darling, Michal Kucera, Christopher M Wade
    posted to phylogeny phylogeography by zwang on 2007-03-23 10:01:27 as **
  • Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
    BMC Bioinformatics, Vol. 8 (09 January 2007), 6.
    by Roger A Craig, Li Liao
    posted to interaction phylogeny prediction protein by zwang on 2007-04-16 13:57:11 as *** along with 2 people marti iris_2001
  • Bayesian support is larger than bootstrap support in phylogenetic inference: a mathematical argument
    Math Med Biol, Vol. 24, No. 4. (1 December 2007), pp. 401-411.
    by Tom Britton, Bodil Svennblad, Per Erixon, Bengt Oxelman
    posted to bayesian bootstrap phylogeny by zwang on 2008-03-16 15:10:59 as *** along with 1 person adacier
  • Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 333-340.
    by SD Dunn, LM Wahl, GB Gloor
    posted to contact interaction mi phylogeny prediction residue by zwang on 2008-05-09 02:44:06 as *** along with 3 people and 1 group bicko sobolevnrm marck baker-group
  • Evidence of Two Lyssavirus Phylogroups with Distinct Pathogenicity and Immunogenicity
    J. Virol., Vol. 75, No. 7. (1 April 2001), pp. 3268-3276.
    by Hassan Badrane, Chokri Bahloul, Pierre Perrin, Noel Tordo
    posted to rabies phylogeny mokola lagos ebl by Zelie on 2008-09-30 15:00:58 as ** along with 1 group Rabies virology
  • Phylogenetic classification and the universal tree.
    Science, Vol. 284, No. 5423. (25 June 1999), pp. 2124-2129.
    by WF Doolittle
    posted to phylogeny by ykadi on 2007-06-26 14:08:35 as ** along with 2 people bayesian eweaver
  • Interpreting the universal phylogenetic tree.
    Proc Natl Acad Sci U S A, Vol. 97, No. 15. (18 July 2000), pp. 8392-8396.
    by CR Woese
    posted to phylogeny by ykadi on 2007-06-26 14:10:03 as ** along with 4 people bayesian gulsacan hdsskin fhsantanna
  • Inferring protein interactions from phylogenetic distance matrices.
    Bioinformatics, Vol. 19, No. 16. (1 November 2003), pp. 2039-2045.
    by J Gertz, G Elfond, A Shustrova, M Weisinger, M Pellegrini, S Cokus, B Rothschild
    posted to inference interaction phylogeny protein by wnpx on 2006-08-24 18:48:09 as ** along with 3 people and 1 group lfriedl balajis ruvido kdl
  • Phylogeny of the arthropod endosymbiont Wolbachia based on the wsp gene
    Insect Molecular Biology, Vol. 8, No. 3. (1999), pp. 399-408.
    by MMM van Meer, J Witteveldt, R Stouthamer
    posted to arthropod bacteria endosymbiont genetic insect parasite phylogeny wolbachia wsp by vhphys on 2008-03-13 13:23:48 as **
  • Application of Combined Morphological-Molecular Approaches to the Identification of Planktonic Protists from Environmental Samples
    The Journal of Eukaryotic Microbiology, Vol. 0, No. ja. (0)
    by Joel R Duff, BALL Hope, Peter J Lavrentyev
    posted to phylogeny plankton protist taxonomy by vaulot on 2008-05-13 02:07:50 as *** along with 2 groups Microbial-Ecology Papers recommended by the Roscoff Plankton Group
  • A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes
    Systematic and Applied Microbiology, Vol. In Press, Corrected Proof
    by Jörg Peplies, Renzo Kottmann, Wolfgang Ludwig, Frank O Glöckner
    posted to sofware phylogeny clone_libraries 16s by vaulot on 2008-09-17 12:49:31 as ** along with 2 groups Papers recommended by the Roscoff Plankton Group Microbial-Ecology
  • A Hierarchical View of Convergent Evolution in Microbial Eukaryotes
    Journal of Eukaryotic Microbiology, Vol. 55, No. 2. (April 2008), pp. 59-68.
    by Brian S Leander
    posted to eukaryote evolution phylogeny by vaulot on 2008-05-13 01:41:50 as *** along with 1 person and 2 groups jdelcampo Microbial-Ecology Papers recommended by the Roscoff Plankton Group
  • Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species.
    Proc Natl Acad Sci U S A (25 February 2008)
    by Cindy Martens, Klaas Vandepoele, Yves Van de Peer
    posted to alveolate eukaryote genome phylogeny by vaulot on 2008-04-28 23:29:25 as ** along with 2 people and 2 groups aconesa cmzmasek Microbial-Ecology Papers recommended by the Roscoff Plankton Group
  • Bosque: Integrated phylogenetic analysis software.
    Bioinformatics (Oxford, England) (1 September 2008)
    by Salvador Ramírez-Flandes, Osvaldo Ulloa
    posted to sofware phylogeny bioinformatics by vaulot on 2008-09-10 07:04:51 as *** along with 4 people and 2 groups cgaugain treangen druvus nuin Papers recommended by the Roscoff Plankton Group Microbial-Ecology
  • A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
    Systematic Biology, Vol. 52, No. 5. (2003), pp. 696-704.
    by Stéphane Guindon, Olivier Gascuel
    posted to bioinformatics phylogeny by urgi on 2007-12-04 15:42:29 as ** along with 1 person timflutre
  • A simple, fast, and accurate method of phylogenomic inference
    Genome Biology, Vol. 9 (13 October 2008), R151.
    by Martin Wu, Jonathan A Eisen
    posted to software phylogeny phylogenomics by treangen on 2008-11-21 09:37:09 as ** along with 8 people and 2 groups cgaugain Katje operon ellakat scryrps djkt aramata druvus microbiology_nijmegen iSEEM
  • Phylogeny.fr: robust phylogenetic analysis for the non-specialist.
    Nucleic acids research (6 May 2008)
    by A Dereeper, V Guignon, G Blanc, S Audic, S Buffet, F Chevenet, J-F F Dufayard, S Guindon, V Lefort, M Lescot, J-M M Claverie, O Gascuel
    posted to webserver software phylogeny phylogenetic analyses by treangen on 2008-11-25 13:03:57 as ** along with 3 people operon druvus sanchezbuelna
  • Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and can not say.
    Molecular biology and evolution (28 October 2008)
    by Seth R R Bordenstein, Charalampos Paraskevopoulos, Julie C C Dunning Hotopp, Panagiotis Sapountzis, Nathan Lo, Claudio Bandi, Hervé Tettelin, John H H Werren, Kostas Bourtzis
    posted to wolbachia trees phylogeny phylogenomic parasitism mutualism by treangen on 2008-11-25 09:24:22 as **
  • Large-scale assignment of orthology: back to phylogenetics?
    Genome Biology, Vol. 9, No. 10. (2008)
    by Toni Gabaldon
    posted to phylogeny ortholog genome by treangen on 2008-11-20 14:00:35 as ** along with 8 people cgaugain GustavoLacerda maximilianh samgj natstreet druvus APRegier barriot
  • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
    Systematic biology, Vol. 56, No. 4. (August 2007), pp. 564-577.
    by G Talavera, J Castresana
    posted to testing sequence protein phylogeny jctalk alignment accuracy 2007 by treangen on 2008-11-23 01:10:53 as ** along with 2 people druvus Patola
  • Reconstructing evolution of sequences subject to recombination using parsimony.
    Mathematical biosciences, Vol. 98, No. 2. (March 1990), pp. 185-200.
    by J Hein
    posted to reconstruction recombination phylogeny parsimony hgt by treangen on 2008-11-25 18:50:02 as **
  • Is multiple-sequence alignment required for accurate inference of phylogeny?
    Syst Biol, Vol. 56, No. 2. (April 2007), pp. 206-221.
    by M Höhl, MA Ragan
    posted to ungapped testing sequence-alignment sequence phylogeny multiple alignment accuracy 2007 by treangen on 2007-07-09 13:17:37 as *** along with 1 person cjeans
  • Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.
    by Morgan N Price, Paramvir S Dehal, Adam P Arkin
    posted to phylogeny orthologs gene bbh bacteria by treangen on 2008-11-27 19:38:15 as ** along with 10 people and 3 groups druvus carlk operon dpollard dquest djkt zwang cabbagezs heliopais blobbybirdman EisenLab cis-regulatory-evolution Myxo group
  • BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.
    Bioinformatics (5 May 2006)
    by Marc A A Suchard, Benjamin D D Redelings
    posted to statistical-alignment software phylogeny mcmc bayesian alignment by treangen on 2008-11-19 13:27:10 as *** along with 5 people and 1 group alexeid aprasad eckart_bindewald indigoviolet AaronDarling EisenLab
  • An assessment of the impacts of molecular oxygen on the evolution of proteomes.
    Molecular biology and evolution, Vol. 25, No. 9. (September 2008), pp. 1931-1942.
    by S Vieira-Silva, EP Rocha
    posted to proteomes phylogeny oxygen evolution aerobes by treangen on 2008-11-21 09:43:00 as **
  • Assessing the accuracy of ancestral protein reconstruction methods.
    PLoS Comput Biol, Vol. 2, No. 6. (23 June 2006)
    by PD Williams, DD Pollock, BP Blackburne, RA Goldstein
    posted to protein phylogeny evolution alignment accuracy 2006 by treangen on 2008-11-22 17:34:01 as ** along with 1 person cjeans
  • Searching for Convergence in Phylogenetic Markov Chain Monte Carlo
    Systematic Biology, Vol. 55, No. 4. (August 2006), pp. 553-565.
    by Beiko, Robert, Keith, Jonathan, Harlow, Timothy, Ragan, Mark
    posted to phylogeny mcmc evolution convergence bayesian by treangen on 2008-11-19 13:05:21 as *** along with 3 people akifumi redelings rsandie
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