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Tag phylogenetics [538 articles]

Recent papers classified by the tag phylogenetics.
  • Phylogenomic inference of protein molecular function: advances and challenges.
    Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 170-179.
    by K Sjölander
    posted to phylogenetics by ziquje on 2005-05-18 22:47:30 as ** along with 3 people sgoetz jwortman sriram_s
  • Molecular evidence for multiple polyploidization and lineage recombination in the Chrysanthemum indicum polyploid complex (Asteraceae)
    New Phytologist, Vol. 171, No. 4. (September 2006), pp. 875-886.
    by Yang, Wenhua, Glover, J Beverley, Rao, Guang-Yuan, Yang, Ji
    posted to phylogenetics polyploidy by yife on 2007-11-14 12:42:20 as ** along with 2 people echinotrix TaqSys
  • Genome-Wide Analysis of the Cyclin Family in Arabidopsis and Comparative Phylogenetic Analysis of Plant Cyclin-Like Proteins
    Plant Physiol., Vol. 135, No. 2. (1 June 2004), pp. 1084-1099.
    by Guanfang Wang, Hongzhi Kong, Yujin Sun, Xiaohong Zhang, Wei Zhang, Naomi Altman, Claude W Depamphilis, Hong Ma
    posted to arabidopsis evolution phylogenetics by xwbcn on 2006-03-25 16:17:27 as ***
  • PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification
    Genome Biology, Vol. 7 (14 September 2006), R83.
    by Nandini Krishnamurthy, Duncan Brown, Dan Kirshner, Kimmen Sjolander
    posted to protein phylogenetics bioinfpdl by Tingting on 2008-06-05 02:02:20 as read along with 1 person cdallett
  • Prokaryotic evolution in light of gene transfer.
    Mol Biol Evol, Vol. 19, No. 12. (December 2002), pp. 2226-2238.
    by JP Gogarten, WF Doolittle, JG Lawrence
    posted to phylogenetics hgt bioinfpdl by Tingting on 2008-05-20 10:32:38 as ** along with 2 people jmeppley AaronDarling
  • Data exploration in phylogenetic inference: scientific, heuristic, or neither
    Cladistics, Vol. 19, No. 5. (2003), pp. 379-418.
    by Taran Grant, Arnold G Kluge
    posted to evolution phylogenetics phylogeny by Thaverkamp on 2008-02-15 10:48:16 as **** along with 1 person knaseanka
  • TreeFam: 2008 Update.
    Nucleic Acids Res (1 December 2007)
    by Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan, Yiran Guo, Jean-Karim K Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert JJ Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin
    posted to webresources phylogenetics methods genetrees by tharris on 2008-06-02 20:17:42 as ** along with 1 person gjuggler
  • Automatic genome-wide reconstruction of phylogenetic gene trees.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev
    posted to workflow phylogenetics methods genetree automation by tharris on 2008-06-02 20:16:23 as ** along with 3 people and 1 group stajich shigepong seitentaisei Berkeley Mycology
  • PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
    by Z Yang
    posted to phylogenetics methods maximumlikelihood by tharris on 2008-06-02 20:15:44 as ** along with 11 people and 3 groups skumagai bjorns chrn chad_davis indigoviolet penka BioNica stajich pv usagi-kirin jmjimenez EisenLab Nie Berkeley Mycology
  • DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony.
    Bioinformatics (Oxford, England) (12 May 2008)
    by André Wehe, Mukul S S Bansal, J Gordon G Burleigh, Oliver Eulenstein
    posted to phylogenetics methods genetree by tharris on 2008-06-02 20:14:40 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • Species divergence and relationships in Stephanomeria (Compositae): PgiC phylogeny compared to prior biosystematic studies
    Am. J. Bot., Vol. 93, No. 3. (1 March 2006), pp. 480-490.
    by Ford, Joongku Lee, Baldwin, Gottlieb
    posted to evolution phylogenetics by TaqSys on 2007-03-01 17:05:07 as ** along with 1 person agg19954
  • Empirical vs Bayesian approach for estimating haplotypes from genotypes of unrelated individuals
    BMC Genetics, Vol. 8 (29 January 2007), 2.
    by Shuying S Li, Jacob J Cheng, Lue P Zhao
    posted to methods phylogenetics by TaqSys on 2007-03-01 16:59:54 as ** along with 1 person agg19954
  • Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
    Science, Vol. 315, No. 5815. (23 February 2007), pp. 1126-1130.
    by C von Mering, P Hugenholtz, J Raes, SG Tringe, T Doerks, LJ Jensen, N Ward, P Bork
    posted to microbiology phylogenetics by TaqSys on 2007-03-01 16:59:14 as ** along with 11 people and 7 groups jlgreen mjetten ana nickluscombe michC bluto agg19954 azazello Thaverkamp larsjuhljensen rvgomes iSEEM Green Lab microbiology_nijmegen structural_bioinformatics Bioinformatics EBI-regulation Microbial-Ecology
  • Molecular and morphological incongruence in European species of Isothecium (Bryophyta)
    Molecular Phylogenetics and Evolution, Vol. 42, No. 3. (March 2007), pp. 700-716.
    by Isabel Draper, Lars Hedenas, Guido W Grimm
    posted to phylogenetics by TaqSys on 2007-03-19 09:03:15 as **
  • The Cardamine pratensis (Brassicaceae) group in the Iberian Peninsula: taxonomy, polyploidy and distribution
    Taxon, Vol. 52, No. 4. (November 2003), pp. 783-802.
    by J Lihova, A Tribsch, K Marhold
    posted to phylogenetics polyploidy by TaqSys on 2007-04-17 07:22:43 as ** along with 1 person echinotrix
  • A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference
    Molecular Phylogenetics and Evolution, Vol. 42, No. 2. (February 2007), pp. 528-542.
    by Mark P Simmons, Li-Bing Zhang, Colleen T Webb, Kai Muller
    posted to methods phylogenetics by TaqSys on 2007-03-01 16:33:44 as ** along with 1 person agg19954
  • Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae)
    Molecular Phylogenetics and Evolution, Vol. 42, No. 2. (February 2007), pp. 347-361.
    by Judith Fehrer, Birgit Gemeinholzer, Jr Chrtek, Siegfried Brautigam
    posted to hybridization phylogenetics by TaqSys on 2007-03-01 16:32:49 as ** along with 2 people echinotrix agg19954
  • A chloroplast DNA phylogeny of eastern Phlox (Polemoniaceae): implications of congruence and incongruence with the ITS phylogeny
    Am. J. Bot., Vol. 89, No. 8. (1 August 2002), pp. 1324-1335.
    by Carolyn J Ferguson, Robert K Jansen
    posted to methods phylogenetics statistics by TaqSys on 2007-09-12 09:54:30 as **
  • Deciphering ancient rapid radiations
    Trends in Ecology & Evolution, Vol. 22, No. 5. (May 2007), pp. 258-265.
    by James B Whitfield, Peter J Lockhart
    posted to phylogenetics speciation by TaqSys on 2007-04-27 16:05:56 as **
  • The relevance of phylogeny to studies of global change
    Trends in Ecology & Evolution, Vol. 22, No. 5. (May 2007), pp. 243-249.
    by Erika J Edwards, Christopher J Still, Michael J Donoghue
    posted to climate_change phylogenetics by TaqSys on 2007-04-27 16:02:13 as **
  • Of clades and clans: terms for phylogenetic relationships in unrooted trees
    Trends in Ecology & Evolution, Vol. 22, No. 3. (March 2007), pp. 114-115.
    by Mark Wilkinson, James O Mcinerney, Robert P Hirt, Peter G Foster, Martin T Embley
    posted to methods phylogenetics phylogeography statistics by TaqSys on 2007-09-28 10:29:44 as ** along with 4 people and 2 groups tny dchughes echinotrix agg19954 G4ID Genetics-of-Gambling
  • Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation
    Ecography, Vol. 31, No. 2. (April 2008), pp. 161-175.
    by Phillips, J Steven, Dudik, Miroslav
    posted to climate_change methods phylogenetics by TaqSys on 2008-04-04 14:41:43 as **
  • Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III
    Am. J. Bot., Vol. 94, No. 3. (1 March 2007), pp. 275-288.
    by Joey Shaw, Edgar B Lickey, Edward E Schilling, Randall L Small
    posted to laboratory methods molecular_markers phylogenetics by TaqSys on 2007-03-31 13:54:15 as **
  • Extensive length variation in the cpDNA trnT-trnF region of hemiparasitic Pedicularis and its phylogenetic implications
    Plant Systematics and Evolution
    by FS Yang, XQ Wang
    posted to methods molecular_markers phylogenetics systematics by TaqSys on 2007-03-16 12:29:48 as **
  • Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability.
    Mol Phylogenet Evol, Vol. 27, No. 2. (May 2003), pp. 185-196.
    by L Després, L Gielly, B Redoutet, P Taberlet
    posted to aflp phylogenetics by TaqSys on 2007-12-12 15:27:49 as **
  • Chromosomal Evolution in the Genus Brachyscome (Asteraceae, Astereae): Statistical Tests Regarding Correlation Between Changes in Karyotype and Habit Using Phylogenetic Information
    Journal of Plant Research, Vol. 112, No. 2. (6 June 1999), pp. 145-161.
    by Kuniaki Watanabe, Tetsukazu Yahara, Tetsuo Denda, Keiko Kosuge
    posted to ecology phylogenetics polyploidy by TaqSys on 2007-09-13 08:26:48 as **
  • The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis
    Am. J. Bot., Vol. 92, No. 1. (1 January 2005), pp. 142-166.
    by Joey Shaw, Edgar B Lickey, John T Beck, Susan B Farmer, Wusheng Liu, Jermey Miller, Kunsiri C Siripun, Charles T Winder, Edward E Schilling, Randall L Small
    posted to methods phylogenetics systematics by TaqSys on 2007-03-12 13:56:37 as **
  • Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
    BMC Evolutionary Biology, Vol. 7 (07 March 2007), 34.
    by Maria E Manetti, Magdalena Rossi, Ana PP Costa, Andrea M Clausen, Marie-Anne Van Sluys
    posted to laboratory methods molecular_markers phylogenetics by TaqSys on 2007-03-09 15:46:07 as **
  • NONUNIFORM PROCESSES OF CHROMOSOME EVOLUTION IN SEDGES (CAREX: CYPERACEAE)
    Evolution, Vol. 61, No. 9. (2007), pp. 2175-2194.
    by Andrew L Hipp
    posted to phylogenetics systematics by TaqSys on 2007-08-31 16:15:42 as **
  • Diverse selective modes among orthologs/paralogs of the chalcone synthase (Chs) gene family of Arabidopsis thaliana and its relative A. halleri ssp. gemmifera
    Molecular Phylogenetics and Evolution, Vol. 44, No. 2. (August 2007), pp. 503-520.
    by Wei-Kuang Wang, Barbara A Schaal, You-Mei Chiou, Noriaki Murakami, Xue-Jen Ge, Chi-Chun Huang, Tzen-Yuh Chiang
    posted to molecular_markers phylogenetics systematics by TaqSys on 2007-08-31 16:14:50 as **
  • Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications
    Molecular Phylogenetics and Evolution, Vol. 44, No. 2. (August 2007), pp. 765-777.
    by Xian-Zhao Kan, Shan-Shan Wang, Xin Ding, Xiao-Quan Wang
    posted to evolution molecular_markers phylogenetics systematics by TaqSys on 2007-08-31 16:14:03 as **
  • Duplication and paralog sorting of RPB2 and RPB1 genes in core eudicots
    Molecular Phylogenetics and Evolution, Vol. 44, No. 2. (August 2007), pp. 850-862.
    by Jie Luo, Nori Yoshikawa, Matthew C Hodson, Benjamin D Hall
    posted to molecular_markers phylogenetics systematics by TaqSys on 2007-08-31 16:12:56 as **
  • Reticulate evolution and phylogeography in Asarum sect. Asiasarum (Aristolochiaceae) documented in internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA
    Molecular Phylogenetics and Evolution, Vol. 44, No. 2. (August 2007), pp. 863-884.
    by Hiroki Yamaji, Tatsuya Fukuda, Jun Yokoyama, Jae-Hong Pak, Chang-Zheng Zhou, Chun-Shu Yang, Kenji Kondo, Takashi Morota, Shuichi Takeda, Hiroshi Sasaki, Masayuki Maki
    posted to evolution hybridization methods molecular_markers phylogenetics systematics by TaqSys on 2007-08-31 16:12:10 as **
  • The evolutionary history of Melianthus (Melianthaceae)
    Am. J. Bot., Vol. 93, No. 7. (1 July 2006), pp. 1052-1064.
    by Peter H Linder, Titus Dlamini, Jack Henning, Anthony G Verboom
    posted to evolution molecular_clock phylogenetics speciation by TaqSys on 2007-03-05 15:17:01 as **
  • Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants
    Molecular Phylogenetics and Evolution, Vol. 44, No. 2. (August 2007), pp. 911-919.
    by Gonzalo N Feliner, Josep A Rossello
    posted to genetics laboratory methods molecular_markers phylogenetics systematics by TaqSys on 2007-08-31 16:06:15 as **
  • Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): implications for phylogenetic studies
    Am. J. Bot., Vol. 94, No. 1. (1 January 2007), pp. 42-46.
    by Katie A Hansen, Linda K Escobar, Lawrence E Gilbert, Robert K Jansen
    posted to evolution genetics hybridization phylogenetics polyploidy by TaqSys on 2007-03-05 14:58:22 as ** along with 1 person echinotrix
  • How should gaps be treated in parsimony? A comparison of approaches using simulation
    Molecular Phylogenetics and Evolution, Vol. 42, No. 3. (March 2007), pp. 817-826.
    by Heath T Ogden, Michael S Rosenberg
    posted to methods phylogenetics systematics by TaqSys on 2007-03-12 12:04:32 as **
  • Reconstructing ancestral character states: a critical reappraisal
    Trends in Ecology & Evolution, Vol. 13, No. 9. (1 September 1998), pp. 361-366.
    by Clifford W Cunningham, Kevin E Omland, Todd H Oakley
    posted to methods phylogenetics statistics teaching by TaqSys on 2008-02-01 09:30:00 as **
  • Selecting Single-Copy Nuclear Genes for Plant Phylogenetics: A Preliminary Analysis for the Senecioneae (Asteraceae)
    Journal of Molecular Evolution, Vol. 66, No. 3. (6 March 2008), pp. 276-291.
    by Inés Álvarez, Andrea Costa, Gonzalo Feliner
    posted to phylogenetics molecular_markers by TaqSys on 2008-05-09 10:47:44 as ** along with 1 person echinotrix
  • Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci
    Am. J. Bot., Vol. 94, No. 2. (1 February 2007), pp. 173-183.
    by Mark E Mort, Jenny K Archibald, Christopher P Randle, Nicholas D Levsen, Ryan T O'Leary, Katarina Topalov, Catherine M Wiegand, Daniel J Crawford
    posted to methods phylogenetics by TaqSys on 2007-03-05 10:40:20 as **
  • Novel motifs in amino acid permease genes from Leishmania
    Biochemical and Biophysical Research Communications, Vol. 325, No. 1. (3 December 2004), pp. 353-366.
    by Martin Akerman, Pninit Shaked-Mishan, Salam Mazareb, Hanne Volpin, Dan Zilberstein
    posted to apicomplexa characterization comparative computational families phylogenetics systems by svdate on 2007-12-05 15:49:50 as *** along with 1 person mariakmejia
  • Quantification of ortholog losses in insects and vertebrates.
    Genome Biology, Vol. 8 (16 November 2007), R242.
    by Stefan Wyder, Evgenia V Kriventseva, Reinhard Schroder, Tatsuhiko Kadowaki, Evgeny M Zdobnov
    posted to bioinformatics comparative orthology phylogenetics by svdate on 2007-12-04 16:37:22 as ** along with 3 people and 2 groups cjeans hpaces hlapp Bioinformatics ParkinsonLab_at_MaRS
  • Gene families: the taxonomy of protein paralogs and chimeras.
    Science, Vol. 278, No. 5338. (24 October 1997), pp. 609-614.
    by S Henikoff, EA Greene, S Pietrokovski, P Bork, TK Attwood, L Hood
    posted to families phylogenetics by svdate on 2007-12-04 16:11:49 as ** along with 2 people and 1 group Einat ruvido structural_bioinformatics
  • Assessment of phylogenomic and orthology approaches for phylogenetic inference
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 815-824.
    by Dutilh, , Van Noort, , van der Heijden, , Boekhout, , Snel, , Huynen,
    posted to orthologs orthology phylogenetics by svdate on 2007-12-04 15:52:57 as *** along with 1 person maximilianh
  • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
    Mol Biol Evol, Vol. 17, No. 4. (April 2000), pp. 540-552.
    by J Castresana
    posted to alignment coccipaper methods phylogenetics by stajich on 2008-04-21 01:28:35 as ** along with 4 people and 1 group cmzmasek aprasad treangen ArtemPankin Berkeley Mycology
  • Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.
    PLoS ONE, Vol. 2 (2007)
    by M Kullberg, B Hallström, U Arnason, A Janke
    posted to est mammal phylogenetics phylogenomics phylogeny by stajich on 2007-09-04 19:00:30 as **
  • Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
    Genome Biology, Vol. 8 (16 July 2007), R141.
    by Matthew W Hahn
    posted to duplication gene_tree phylogenetics reconciliation by stajich on 2007-10-03 22:40:49 as *** along with 1 group Berkeley Mycology
  • An Improved General Amino Acid Replacement Matrix
    Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320.
    by Si Q Le, Olivier Gascuel
    posted to protein_evolution phylogenetics molecular_evolution methods evolution bioinformatics by stajich on 2008-06-14 07:08:00 as ** along with 1 person and 1 group friendpine Berkeley Mycology
  • Incorporating Indel Information into Phylogeny Estimation for Rapidly Emerging Pathogens
    BMC Evolutionary Biology, Vol. 7 (14 March 2007), 40.
    by Benjamin D Redelings, Marc A Suchard
    posted to alignment evolution gene indels phylogenetics by stajich on 2007-04-19 22:09:16 as *** along with 2 people and 1 group aprasad dpollard EisenLab
  • Evaluation of the models handling heterotachy in phylogenetic inference
    BMC Evolutionary Biology, Vol. 7 (01 November 2007), 206.
    by Yan Zhou, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe
    posted to heterotachy methods phylogenetics phylogenomics by stajich on 2007-11-07 04:18:59 as ** along with 1 group Berkeley Mycology
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