Tag phylogenetics [at least 200 articles] Export

Recent papers classified by the tag phylogenetics.

	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 (6 November 2009), esp086. by Genome 10K Community of Scientists posted to phylogenetics genomics by aprasad on 2009-11-06 19:20:25 as
	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 uk transmission spatial phylogenetics migration hiv genetic-diversity clustering 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 3 people 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 uk phylogenetics parameters msm migration hiv history finding-parameters 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 dynamics 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 1 person 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 28 people and 3 groups 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 32 people and 2 groups 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
	Phylodynamics of Infectious Disease Epidemics. [My Copy] Genetics (21 September 2009) by Erik M. Volz, Sergei L. Kosakovsky Pond, Melissa J. Ward, Andrew J. Leigh Brown, Simon D. Frost posted to phylogenetics molecular-typing differential-equation-model compartmental-model coalescence clustering by tronella on 2009-10-15 12:37:36 as
	The neighbor-joining method: a new method for reconstructing phylogenetic trees. [My Copy] Molecular biology and evolution, Vol. 4, No. 4. (1 July 1987), pp. 406-425. by N. Saitou, M. Nei posted to phylogenetics by qiang on 2009-10-15 08:01:10 as along with 17 people and 1 group vtraag parnell esyoun forest2087 aprasad mount_misery cawelsh9 cen4ik sandra_yu greger_halltorp taka gelack BioNica usagi-kirin ArtemPankin bandrewfox Auger Dead 60's
	Estimating maximum likelihood phylogenies with PhyML. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 537 (2009), pp. 113-137. by Stéphane Guindon, Frédéric Delsuc, Jean-François F. Dufayard, Olivier Gascuel posted to software phylogenetics by skembel on 2009-10-15 00:09:03 as
	Animal evolution and the molecular signature of radiations compressed in time. [My Copy] Science (New York, N.Y.), Vol. 310, No. 5756. (23 December 2005), pp. 1933-1938. by Antonis Rokas, Dirk Krüger, Sean B. Carroll posted to speciation rokas polytomy phylogenomics phylogenetics metazoan_phylogeny by biomcgary on 2009-10-13 20:39:43 as along with 4 people soberhaensli operon bayesian tny
	Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. [My Copy] Nature reviews. Genetics, Vol. 3, No. 5. (May 2002), pp. 380-390. by Noah A. Rosenberg, Magnus Nordborg posted to phylogenetics partner-distribution evolution coalescence by tronella on 2009-10-12 11:13:12 as along with 3 people lizbiogen ilyashl ArtemPankin
	Automatic genome-wide reconstruction of phylogenetic gene trees [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i549-558. by Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev posted to proteins phylogenetics duplication by djkt on 2009-10-09 16:29:19 as along with 7 people and 1 group biomcgary thegoose2 gjuggler stajich shigepong seitentaisei tharris Mycology
	PAML 4: phylogenetic analysis by maximum likelihood. [My Copy] Molecular biology and evolution, Vol. 24, No. 8. (1 August 2007), pp. 1586-1591. by Ziheng Yang posted to phylogenetics phylogenetic_methods by biomcgary on 2009-10-08 22:00:16 as along with 13 people and 1 group ckenaley michaelbarton dquest druvus operon akifumi hdopazo BioNica stajich ryanraaum RamuAnandakrishnan CharlesM Ema Mycology
	RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees [My Copy] Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 456-463. by A. Stamatakis, T. Ludwig, H. Meier posted to phylogenetics phylogenetic_methods maximum_likelihood by biomcgary on 2009-10-08 21:56:22 as along with 3 people operon marck polpotak
	Sequence analysis and phylogenetic relationship of genes encoding heterodimeric phospholipases A2 from the venom of the scorpion Anuroctonus phaiodactylus [My Copy] Gene, Vol. 396, No. 1. (01 July 2007), pp. 149-158. by Norma A. Valdez-Cruz, Lorenzo Segovia, Miguel Corona, Lourival D. Possani posted to phylogenetics phospholipase anuroctonus a2 by cazmantis on 2009-10-07 18:56:14 as
	The merging of community ecology and phylogenetic biology. [My Copy] Ecology letters, Vol. 12, No. 7. (July 2009), pp. 693-715. by Jeannine Cavender-Bares, Kenneth H. Kozak, Paul V. Fine, Steven W. Kembel posted to phylogenetics phylodiversity community_ecology community by skembel on 2009-10-05 05:55:31 as along with 1 person maren
	Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. [My Copy] Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Vol. 363, No. 1512. (27 December 2008), pp. 4013-4021. by Mark T. Holder, Derrick J. Zwickl, Christophe Dessimoz posted to phylogenetics by gjuggler on 2009-10-02 10:30:19 as along with 1 person operon
	The human protein coevolution network. [My Copy] Genome research, Vol. 19, No. 10. (20 October 2009), pp. 1861-1871. by Elisabeth R. Tillier, Robert L. Charlebois posted to sysbio proteins phylogenetics evolution by djkt on 2009-10-01 23:58:20 as along with 7 people dfdong Garamonfok venancio jperkins TRHvidsten phoenixzxl tmmurali
	Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus [My Copy] Genome Biol Evol, Vol. 2009, No. 0. (23 September 2009), pp. 325-339. by Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke, J. Peter Gogarten posted to phylogenetics microbes ecology by djkt to the group iSEEM on 2009-10-01 00:13:13 as along with 1 person skembel

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evolution	572
selection	227
mutation	198
methods	139
genomics	112
tree	101
bioinformatics	94
phylogenomics	77
phylogeny	57
alignment	55
software	54
bayesian	51
mammal	46
review	44
transposon	42
metagenomics	35
method	33
tools	29
master	28
algorithm	27
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
rare_genomic_characters	16
database	15
duplication	15
molecular_clock	15
protein	15
systematics	15
bioinformatics_software	14
comparative_genomics	14
parsimony	14
ploscb08	14
comparative	13
recombination	13
simulation	13
horizontal_transfer	12
molecular_evolution	12
platyrrhini	12
polyploidy	12
retroelement	12
bat	11
gene_tree	11
horizontal-gene-transfer	11
mcmc	11
microbes	11
sequence	11
virus	11
ecology	10
speciation	10
statistics	10
annotation	9
molecular_markers	9
nsfprop	9
protein-protein_interaction	9
root_eutheria	9
tree_visualization	9
visualization	9
classification	8
coalescence	8
community	8
comparative-genomics	8
comparative-sequence-analysis	8
hiv	8
long_branch_attraction	8
model-selection	8
molecular	8
mrbayes	8
msa	8
similarity	8
supertree	8
theria	8
tree-of-life	8
analysis	7
archaea	7
codon_bias	7
congruence_landscapes	7
functional	7
metazoa	7
rna	7
support	7
taxonomy	7
yeast	7

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