Tag phylogenetics [at least 200 articles] Export

Recent papers classified by the tag phylogenetics.

	The causes and consequences of HIV evolution. [My Copy] Nature reviews. Genetics, Vol. 5, No. 1. (January 2004), pp. 52-61. by Andrew Rambaut, David Posada, Keith A. Crandall, Edward C. Holmes posted to within-host subtype recombination phylogenetics immune-selection hiv genetic-diversity evolution-rate evolution drug-resistance cross-species by tronella on 2009-11-23 12:21:26 as along with 2 people KevinVanCalster bmaust
	Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny [My Copy] Mol Biol Evol, Vol. 25, No. 1. (1 January 2008), pp. 83-91. by E. Bapteste, E. Susko, J. Leigh, I. Ruiz-Trillo, J. Bucknam, W. F. Doolittle posted to phylogenetics evolution by operon on 2009-11-20 20:46:03 as
	Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups [My Copy] Cladistics, Vol. 25, No. 3. (2009), pp. 211-230. by Pablo A. Goloboff, Santiago A. Catalano, J. Marcos Mirande, et al.Claudia A. Szumik, J. Salvador Arias, Mari Källersjö, James S. Farris posted to tree supertree supermatrix phylogenomics phylogenetics by aprasad on 2009-11-20 20:43:07 as
	Human immunodeficiency virus type 1 subtypes prevalence in central China. [My Copy] Yonsei medical journal, Vol. 50, No. 5. (31 October 2009), pp. 644-649. by Fei Zhao, Zhe Wang, Wen-Jie J. Li posted to phylogenetics molecular-typing hiv china by tronella on 2009-11-20 14:58:42 as
	A HIV-1 heterosexual transmission chain in Guangzhou, China: a molecular epidemiological study. [My Copy] Virology journal, Vol. 6 (25 September 2009), 148. by Zhigang Han, Tommy W. Leung, Jinkou Zhao, et al.Ming Wang, Lirui Fan, Kai Li, Xinli Pang, Zhenbo Liang, Wilina W. Lim, Huifang Xu posted to sex-workers phylogenetics molecular-typing hiv heterosexual china by tronella on 2009-11-20 14:46:49 as
	Population Dynamics of HIV-1 Inferred From Gene Sequences [My Copy] Genetics, Vol. 151, No. 2. (1 February 1999), pp. 427-438. by Nicholas C. Grassly, Paul H. Harvey, Edward C. Holmes posted to variable-infectivity uncertainty subtype rate population-movement phylogenetics mutation hiv genetic-diversity finding-parameters effective-population-size drug-resistance coalescence by tronella on 2009-11-20 14:34:41 as
	Molecular clocks: when timesare a-changin' [My Copy] Trends in Genetics, Vol. 22, No. 2. (February 2006), pp. 79-83. by S. Ho, G. Larson posted to phylogenetics molecular_clock evolution by operon on 2009-11-17 01:39:05 as
	A phylogenomic approach to resolve the basal pterygote divergence. [My Copy] Molecular biology and evolution, Vol. 26, No. 12. (December 2009), pp. 2719-2730. by Sabrina Simon, Sascha Strauss, Arndt von Haeseler, Heike Hadrys posted to transposon phylogenetics phylogenetic_analyses genomics evolution by operon on 2009-11-17 00:27:09 as
	Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation [My Copy] Bioinformatics, Vol. 24, No. 23. (1 December 2008), pp. 2713-2719. by Jean-Marie Cornuet, Filipe Santos, Mark A. Beaumont, et al.Christian P. Robert, Jean-Michel Marin, David J. Balding, Thomas Guillemaud, Arnaud Estoup posted to software phylogenetics evolution bioinformatics by operon on 2009-11-16 20:23:06 as
	Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine [My Copy] PLoS ONE, Vol. 4, No. 8. (20 August 2009), e6669. by Marcus J. Claesson, Orla O'Sullivan, Qiong Wang, et al.Janne Nikkilä, Julian R. Marchesi, Hauke Smidt, Willem M. de Vos, R. Paul Ross, Paul W. O'Toole posted to pyrosequencing phylogenetics metagenomics bootstrap by skembel to the group iSEEM on 2009-11-15 18:23:10 as along with 2 people nnnagara neils
	Reconstructing the History of Yeast Genomes [My Copy] PLoS Genet, Vol. 5, No. 5. (15 May 2009), e1000483. by David Sankoff posted to yeast phylogenetics genomes by eannaokeefe on 2009-11-12 14:54:53 as along with 2 people emptyhb djkt
	Global Microsatellite Content Distinguishes Humans, Primates, Animals, and Plants [My Copy] Mol Biol Evol, Vol. 26, No. 12. (1 December 2009), pp. 2809-2819. by C. L. Galindo, L. J. McIver, J. F. McCormick, et al.M. A. Skinner, Y. Xie, R. A. Gelhausen, K. Ng, N. M. Kumar, H. R. Garner posted to repeats phylogenetics kmer arrays by djkt on 2009-11-11 00:45:24 as
	TOPD/FMTS: a new software to compare phylogenetic trees [My Copy] Bioinformatics, Vol. 23, No. 12. (25 April 2007), pp. btm135-1558. by Pere Puigbo, Santiago Garcia-Vallve, James O. McInerney posted to phylogenetics by gjuggler on 2009-11-09 10:02:54 as along with 6 people vallve sharpton BioNica druvus dparks tny
	Inferring Population History from Molecular Phylogenies [My Copy] Philosophical Transactions: Biological Sciences, Vol. 349, No. 1327. (1995), pp. 25-31. by Sean Nee, Eddie C. Holmes, Andrew Rambaut, Paul H. Harvey posted to population-size phylogenetics coalescence by tronella on 2009-11-06 19:58:02 as
	Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species [My Copy] J Hered, Vol. 100, No. 6. (1 November 2009), pp. 659-674. by Genome 10K Community of Scientists posted to phylogenetics genomics by aprasad on 2009-11-06 19:20:25 as along with 3 people seb1 coela kiekyon
	Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences [My Copy] Mol Biol Evol, Vol. 22, No. 5. (1 May 2005), pp. 1185-1192. by A. J. Drummond, A. Rambaut, B. Shapiro, O. G. Pybus posted to skyline phylogenetics hepatitis finding-parameters evolution-rate egypt demographics coalescence by tronella on 2009-11-05 22:22:33 as along with 4 people carpi druvus ryanraaum cstrasser
	Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 40. (6 October 2009), pp. 17077-17082. by Gregory E. Sims, Se-Ran R. Jun, Guohong Albert A. Wu, Sung-Hou H. Kim posted to phylogenetics mammals kmer alignment by djkt on 2009-11-04 22:44:52 as along with 7 people wendygarnica Geknitics jsatkosk mkiyer antariksh sujaikumar bpcusack
	Distributions of Tree Comparison Metrics--Some New Results [My Copy] Syst Biol, Vol. 42, No. 2. (1 June 1993), pp. 126-141. by Mike A. Steel, David Penny posted to phylogenetics methods by skembel to the group iSEEM on 2009-11-04 19:13:37 as
	Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. [My Copy] Journal of virology, Vol. 81, No. 23. (December 2007), pp. 13050-13056. by Robert J. Gifford, Tulio de Oliveira, Andrew Rambaut, et al.Oliver G. Pybus, David Dunn, Anne-Mieke M. Vandamme, Paul Kellam, Deenan Pillay, UK Collaborative Group on HIV Drug Resistance posted to transmission spatial phylogenetics migration hiv genetic-diversity clustering britain by tronella on 2009-11-04 19:05:07 as
	Assessing the Effects of Human Mixing Patterns on Human Immunodeficiency Virus-1 Interhost Phylogenetics Through Social Network Simulation [My Copy] Genetics, Vol. 172, No. 4. (1 April 2006), pp. 2033-2045. by Steven M. Goodreau posted to phylogenetics model-comparison hiv genetic-diversity core-group assortativity by tronella on 2009-11-04 18:27:58 as
	Stratification of co-evolving genomic groups using ranked phylogenetic profiles [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 355. by Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka, Christos Ouzounis posted to phylogenomics phylogenetics genomic_signatures comparative_genomics bioinformatics_software bioinformatics by CLH_1865 on 2009-11-02 20:10:15 as along with 2 people and 1 group stajich druvus Mycology
	Phylogenomics of primates and their ancestral populations [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 1929-1941. by Adam Siepel posted to review primates popgen phylogenetics evolution by djkt on 2009-11-02 19:00:34 as along with 2 people aprasad merpublic
	Supertrees join the mainstream of phylogenetics [My Copy] Trends in Ecology & Evolution, Vol. 24, No. 1. (18 January 2009), pp. 1-3. by J. Cotton, M. Wilkinson posted to phylogenetics history hierarchy evolution by livingthingdan on 2009-10-31 01:48:30 as along with 4 people calderonv inquil anphony skembel
	phyloXML: XML for evolutionary biology and comparative genomics [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 356. by Mira Han, Christian Zmasek posted to phylogenetics evolution bioinformatics by operon on 2009-10-31 00:46:06 as along with 6 people and 1 group cisevol kshameer Geknitics druvus phoenixzxl cmzmasek BergmanLab
	Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. [My Copy] Journal of molecular evolution, Vol. 39, No. 3. (September 1994), pp. 306-314. by Z. Yang posted to phylogenetics evolution by operon on 2009-10-31 00:45:45 as along with 3 people nuin gjuggler bpb
	Rooting with Multiple Outgroups: Consensus Versus Parsimony [My Copy] Cladistics, Vol. 14, No. 2. (1998), pp. 193-200. by Véronique Barriel, Pascal Tassy posted to phylogenetics evolution by operon on 2009-10-31 00:45:42 as along with 1 person nuin
	Multiple Sequence Alignment in Phylogenetic Analysis [My Copy] Molecular Phylogenetics and Evolution, Vol. 16, No. 3. (September 2000), pp. 317-330. by A. Phillips posted to phylogenetics evolution by operon on 2009-10-31 00:45:39 as along with 4 people nuin aprasad ziquje stormybriggs
	The Information Content of a Character under a Markov Model of Evolution [My Copy] Molecular Phylogenetics and Evolution, Vol. 17, No. 2. (November 2000), pp. 231-243. by M. Shpak posted to phylogenetics evolution by operon on 2009-10-31 00:45:36 as along with 1 person nuin
	Estimating the Transition/Transversion Ratio from Independent Pairwise Comparisons with an Assumed Phylogeny [My Copy] Journal of Molecular Evolution, Vol. 44, No. 1. (24 January 1997), pp. 112-119. by Andy Purvis, Lindell Bromham posted to phylogenetics evolution by operon on 2009-10-31 00:45:33 as along with 1 person nuin
	Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology [My Copy] Science, Vol. 294, No. 5550. (14 December 2001), pp. 2310-2314. by John P. Huelsenbeck, Fredrik Ronquist, Rasmus Nielsen, Jonathan P. Bollback posted to phylogenetics evolution by operon on 2009-10-31 00:45:29 as along with 9 people and 1 group nuin seanyuan aprasad madhurjyag renewang bourscheid eustatic tny spavey FAB-lab
	Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 12. (22 March 2005), pp. 4425-4429. by StÃ©phane HuÃ©, Deenan Pillay, Jonathan P. Clewley, Oliver G. Pybus posted to phylogenetics parameters msm migration hiv history finding-parameters britain by tronella on 2009-10-30 20:03:06 as
	Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics [My Copy] PLoS Med, Vol. 5, No. 3. (18 March 2008), e50. by Fraser Lewis, Gareth J. Hughes, Andrew Rambaut, Anton Pozniak, Andrew J. Leigh Brown posted to phylogenetics phylodynamics msm hiv dynamic drug-resistance clustering britain by tronella on 2009-10-30 19:00:59 as
	Phylo-evo-devo: combining phylogenetics with evolutionary developmental biology [My Copy] BMC Biology, Vol. 7, No. 1. (2009), 36. by Alessandro Minelli posted to review phylogenetics evo-devo commentary by cmzmasek on 2009-10-29 22:14:52 as along with 2 people aaltenburger cisevol
	Regeneration traits are structuring phylogenetic diversity in cork oak (<i>Quercus suber</i>) woodlands [My Copy] Journal of Vegetation Science, Vol. 20, No. 6. (2009), pp. 1009-1015. by Manuel Coca, Juli G. Pausas posted to traits suber regeneration quercus_suber quercus phylogenetics phylodiversity mediterranean iberian_peninsula ecology diversity cork_oak by pausas on 2009-10-29 19:53:20 as
	Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences [My Copy] Systematic Zoology, Vol. 28, No. 2. (1979), pp. 132-163. by Morris Goodman, John Czelusniak, G. William Moore, A. E. Romero Herrera, Genji Matsuda posted to phylogenetics parsimony congruence by aprasad on 2009-10-29 18:27:54 as
	THE POPULATION BIOLOGY OF MITOCHONDRIAL DNA AND ITS PHYLOGENETIC IMPLICATIONS [My Copy] Annual Review of Ecology, Evolution, and Systematics, Vol. 36, No. 1. (2005), pp. 621-642. by William, David M. Rand posted to phylogenetics mitochondrial_dna by lizbiogen on 2009-10-29 16:13:23 as along with 1 person druvus
	Genome-scale approaches to resolving incongruence in molecular phylogenies [My Copy] Nature, Vol. 425, No. 6960. (23 October 2003), pp. 798-804. by Antonis Rokas, Barry L. Williams, Nicole King, Sean B. Carroll posted to phylogenetics incongruence genomes by skembel to the group iSEEM on 2009-10-28 20:32:38 as along with 7 people biomcgary nlapalu druvus knaseanka aprasad AaronDarling srfairclough
	Phylogenetic analysis of modularity in protein interaction networks. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (14 October 2009), 333. by Sinan Erten, Xin Li, Gurkan Bebek, Jing Li, Mehmet Koyutürk posted to systems_biology protein_interaction protein-protein_interaction phylogenomics phylogenetics network_evolution module_rewiring module by biomcgary on 2009-10-28 18:46:31 as along with 7 people and 2 groups sillitoe ppgardne grahamc zwang druvus barriot phoenixzxl Orengo Group Journal Picks Journal picks
	Mitochondrial Insertions into Primate Nuclear Genomes Suggest the Use of numts as a Tool for Phylogeny [My Copy] Mol Biol Evol, Vol. 26, No. 10. (1 October 2009), pp. 2175-2179. by Einat Hazkani-Covo posted to rare_genomic_characters phylogenetics numts by aprasad on 2009-10-27 22:49:53 as
	An exploratory study on the social and genotypic clustering of HIV infection in men having sex with men. [My Copy] AIDS (London, England), Vol. 23, No. 13. (24 August 2009), pp. 1755-1764. by Shui Shan S. Lee, Dennise K. Tam, Yi Tan, et al.Wai Lai L. Mak, Ka Hing H. Wong, Jonathan H. Chen, Wing Cheong C. Yam posted to spatial phylogenetics msm hong-kong hiv clustering by tronella on 2009-10-27 13:53:09 as
	Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis [My Copy] Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635. by Ari Loytynoja, Nick Goldman posted to phylogenetics evolution alignment algorithm by operon on 2009-10-26 18:17:31 as along with 29 people and 3 groups memerman TRHvidsten BioNica cmzmasek timflutre pradiptaray alexeid marti bpcusack hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology aprasad zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
	MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (1 September 2009), 274. by Torsten Blum, Sebastian Briesemeister, Oliver Kohlbacher posted to phylogenetics by operon on 2009-10-26 04:56:20 as along with 1 person ptrobajo
	Alignment Uncertainty and Genomic Analysis [My Copy] Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476. by Karen M. Wong, Marc A. Suchard, John P. Huelsenbeck posted to phylogenetics genomics bioinformatics alignment_methods alignment algorithm by operon on 2009-10-25 06:08:29 as along with 33 people and 2 groups Jporci walshtp darian ptrobajo friendpine skembel druvus treangen bpb aprasad dayjm pradiptaray dpollard tny djkt cjeans zwang lisa1 cactus biomcgary lilou dandaman gjuggler renatomilani mclarenv youdon bpcusack guhjy jdelcampo adacier gracio timflutre jfr EisenLab microbiology_nijmegen
	The insect cytochrome oxidase I gene: evolutionary patterns and conserved primers for phylogenetic studies [My Copy] Insect Molecular Biology, Vol. 5, No. 3. (1996), pp. 153-165. by D. H. Lunt, D. X. Zhang, J. M. Szymura, O. M. Hewltt posted to phylogenetics patterns evolution arthropod by operon on 2009-10-25 06:06:27 as along with 1 person lizbiogen
	Molecular characterization of picobirnaviruses from new hosts. [My Copy] Virus research, Vol. 143, No. 1. (July 2009), pp. 134-136. by Maria Clara Duarte C. Fregolente, Erich de Castro-Dias, Sandra Soares S. Martins, Fernando Rosado R. Spilki, Silmara Marques M. Allegretti, Maria Silvia Viccari S. Gatti posted to picobirnavirus phylogenetics molecular by dayjm on 2009-10-23 15:19:19 as
	Genome size in Hieracium subgenus Hieracium (Asteraceae) is strongly correlated with major phylogenetic groups [My Copy] Ann Bot, Vol. 104, No. 1. (1 July 2009), pp. 161-178. by Jindrich Chrtek, Jaroslav Zahradnicek, Karol Krak, Judith Fehrer posted to phylogenetics genome_size by echinotrix on 2009-10-22 08:57:18 as
	A tenth crucial question regarding model use in phylogenetics. [My Copy] Trends in ecology & evolution (Personal edition), Vol. 22, No. 10. (October 2007), pp. 509-510. by J. Gatesy posted to phylogenetics model-based bioinformatic by ckenaley on 2009-10-21 04:15:08 as along with 1 person bpcusack
	Model use in phylogenetics: nine key questions [My Copy] Trends in Ecology & Evolution, Vol. 22, No. 2. (February 2007), pp. 87-94. by Scot A. Kelchner, Michael A. Thomas posted to phylogenetics molecular model-based inference evolution by ckenaley on 2009-10-21 04:11:33 as along with 6 people and 2 groups inquil renewang aprasad dchughes russelld bpcusack G4ID Genetics-of-Gambling
	The Importance of Proper Model Assumption in Bayesian Phylogenetics [My Copy] Syst Biol, Vol. 53, No. 2. (1 April 2004), pp. 265-277. by Alan R. Lemmon, Emily C. Moriarty posted to phylogenetics models bionformatics by ckenaley on 2009-10-21 01:48:23 as along with 1 person aprasad
	Phylogenomics: evolution and genomics intersection. [My Copy] International journal of bioinformatics research and applications, Vol. 5, No. 5. (2009), pp. 548-563. by Virendra S. Gomase, Somnath Tagore posted to review phylogenomics phylogenetics by aprasad on 2009-10-15 21:34:55 as

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evolution	579
selection	227
mutation	199
methods	139
genomics	114
tree	102
bioinformatics	96
phylogenomics	79
phylogeny	57
alignment	55
software	55
bayesian	51
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review	44
transposon	44
metagenomics	36
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master	28
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congruence	27
doctorate	27
drosophila	26
likelihood	24
model	23
prokaryote	23
arthropod	22
bacteria	21
bayes	20
diversity	20
maximum-likelihood	20
fungi	18
indel	18
primate	18
genome	17
ortholog	17
proteins	17
clustering	16
gene	16
genetics	16
molecular_clock	16
rare_genomic_characters	16
comparative_genomics	15
database	15
duplication	15
protein	15
systematics	15
bioinformatics_software	14
parsimony	14
ploscb08	14
recombination	14
comparative	13
simulation	13
hiv	12
horizontal_transfer	12
molecular_evolution	12
platyrrhini	12
polyploidy	12
retroelement	12
bat	11
ecology	11
gene_tree	11
horizontal-gene-transfer	11
mcmc	11
microbes	11
sequence	11
statistics	11
virus	11
speciation	10
annotation	9
coalescence	9
molecular_markers	9
nsfprop	9
protein-protein_interaction	9
root_eutheria	9
supertree	9
tree_visualization	9
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comparative-genomics	8
comparative-sequence-analysis	8
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model-selection	8
molecular	8
mrbayes	8
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theria	8
tree-of-life	8
yeast	8
analysis	7
archaea	7
codon_bias	7
congruence_landscapes	7
evolutionary_genomics	7
metazoa	7
rna	7
support	7
taxonomy	7

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