Tag phylogeny [at least 200 articles] Export

Recent papers classified by the tag phylogeny.

	A maximum likelihood framework for protein design [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (29 June 2006), 326. by Claudia Kleinman, Nicolas Rodrigue, Cecile Bonnard, Herve Philippe, Nicolas Lartillot posted to udem stuff robert-cedergren-center phylogeny clique bioinformatics by seb1 on 2009-11-07 23:15:13 as
	THE MACROEVOLUTIONARY DYNAMICS OF ANT DIVERSIFICATION [My Copy] Evolution, Vol. 63, No. 11. (2009), pp. 3023-3030. by Marcio R. Pie, Marcel K. Tschá posted to phylogeny diversification ants by maren on 2009-11-07 00:44:05 as
	Inferring Phylogenies [My Copy] (04 September 2003) by Joseph Felsenstein posted to phylogeny phylogenetic_trees dna biology by vtraag on 2009-11-06 12:13:47 as along with 10 people and 2 groups nuttpo ilyashl aprasad rw294 gjuggler bayesian dpollard cmm farhat dlizcano EisenLab FAB-lab
	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 phylogeny phylogenetic_trees nj neighbour_joining dna biology by vtraag on 2009-11-06 12:10:47 as along with 17 people and 1 group qiang parnell esyoun forest2087 aprasad mount_misery cawelsh9 cen4ik sandra_yu greger_halltorp taka gelack BioNica usagi-kirin ArtemPankin bandrewfox Auger Dead 60's
	A note on the neighbor-joining algorithm of Saitou and Nei. [My Copy] Molecular biology and evolution, Vol. 5, No. 6. (November 1988), pp. 729-731. by J. A. Studier, K. J. Keppler posted to phylogeny phylogenetic_trees nj neighbour_joining dna biology by vtraag on 2009-11-06 12:10:18 as
	Neighbor-Joining Revealed [My Copy] Mol Biol Evol, Vol. 23, No. 11. (1 November 2006), pp. 1997-2000. by Olivier Gascuel, Mike Steel posted to phylogeny phylogenetic_trees nj neighbour_joining dna biology by vtraag on 2009-11-06 12:05:59 as along with 4 people vingron tny rhyax ArtemPankin
	Genome phylogeny based on gene content. [My Copy] Nature genetics, Vol. 21, No. 1. (January 1999), pp. 108-110. by B. Snel, P. Bork, M. A. Huynen posted to these phylogeny paralogy horizontal_gene_transfer by calderonv on 2009-11-05 16:37:45 as along with 1 person maximilianh
	SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics [My Copy] BMC Evolutionary Biology, Vol. 7, No. Suppl 1. (2007) by Beatrice Roure, Naiara R. Ezpeleta, Herve Philippe posted to tree these software phylogeny by calderonv on 2009-11-05 16:34:41 as along with 7 people treangen natstreet druvus operon aprasad akifumi dmp
	Missing data and the design of phylogenetic analyses [My Copy] Journal of Biomedical Informatics In Phylogenetic Inferencing: Beyond Biology, Vol. 39, No. 1. (February 2006), pp. 34-42. by John J. Wiens posted to tree these phylogeny by calderonv on 2009-11-05 16:32:58 as along with 2 people and 1 group skembel aprasad iSEEM
	SHOT: a web server for the construction of genome phylogenies [My Copy] Trends in Genetics, Vol. 18, No. 3. (01 March 2002), pp. 158-162. by J. Korbel, B. Snel, M. Huynen, P. Bork posted to tree these phylogeny metho by calderonv on 2009-11-05 16:04:06 as along with 1 person maximilianh
	A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. [My Copy] Molecular Biology and Evolution, Vol. 18, No. 5. (1 May 2001), pp. 691-699. by S. Whelan, N. Goldman posted to tree these phylogeny maximum-likelihood by calderonv on 2009-11-05 15:58:29 as along with 7 people BioNica michaelbarton bpb chrn ssgong gjuggler gisle
	GARD: a genetic algorithm for recombination detection [My Copy] Bioinformatics, Vol. 22, No. 24. (15 December 2006), pp. 3096-3098. by Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, Christopher H. Woelk, Simon D. W. Frost posted to these recombination phylogeny by calderonv on 2009-11-05 15:51:52 as along with 1 person operon
	The challenge of constructing large phylogenetic trees. [My Copy] Trends Plant Sci, Vol. 8, No. 8. (August 2003), pp. 374-379. by M. J. Sanderson, A. C. Driskell posted to tree these phylogeny by calderonv on 2009-11-05 13:45:39 as along with 1 person and 1 group rvosa FAB-lab
	Matrix Representation of Trees, Redundancy, and Weighting [My Copy] Systematic Biology, Vol. 45, No. 2. (1996), pp. 247-253. by Fredrik Ronquist posted to tree these phylogeny matrix_representation by calderonv on 2009-11-05 13:44:19 as
	Comparison of phylogenetic trees [My Copy] Mathematical Biosciences, Vol. 53, No. 1-2. (February 1981), pp. 131-147. by D. F. Robinson, L. R. Foulds posted to tree these phylogeny by calderonv on 2009-11-05 13:42:15 as along with 5 people druvus alexeid jmeppley balicea blindAngle
	A Modification to Baum and Ragan's Method for Combining Phylogenetic Trees [My Copy] Systematic Biology, Vol. 44, No. 2. (1995), pp. 251-255. by Andy Purvis posted to tree these phylogeny by calderonv on 2009-11-05 13:38:24 as
	Matrix representation with parsimony, taxonomic congruence, and total evidence. [My Copy] Systematic biology, Vol. 51, No. 1. (February 2002), pp. 151-155. by Davide Pisani, Mark Wilkinson posted to these phylogeny matrix_representation by calderonv on 2009-11-05 13:37:02 as
	Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 8. (13 April 1999), pp. 4285-4288. by Matteo Pellegrini, Edward M. Marcotte, Michael J. Thompson, David Eisenberg, Todd O. Yeates posted to tree these profile phylogeny evolution by calderonv on 2009-11-05 13:31:52 as along with 15 people and 1 group jperkins pablocarb chica skembel Robinder dragonrez bicko lfriedl balajis opheliav tny ruvido winterschlaefer shung carlk kdl
	Modeling the evolution of protein domain architectures using maximum parsimony. [My Copy] Journal of molecular biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315. by Jessica H. Fong, Lewis Y. Geer, Anna R. Panchenko, Stephen H. Bryant posted to tree these phylogeny evolution domain by calderonv on 2009-11-05 13:29:44 as along with 8 people and 3 groups wiedenhoeft jameswasmuth icases marcius tny choonpeng redelings zwang BioinfoCIPF SGU-CIPF TNT
	Phylogenetic Analysis Under Dollo's Law [My Copy] Systematic Zoology, Vol. 26, No. 1. (1977), pp. 77-88. by James S. Farris posted to tree these phylogeny by calderonv on 2009-11-05 13:24:21 as
	The supermatrix approach to systematics [My Copy] Trends in Ecology & Evolution, Vol. 22, No. 1. (January 2007), pp. 34-41. by A. Dequeiroz, J. Gatesy posted to tree these supermatrix phylogeny by calderonv on 2009-11-05 11:44:41 as along with 4 people and 3 groups inquil druvus skembel dchughes iSEEM G4ID Genetics-of-Gambling
	Phylogenomics and the reconstruction of the tree of life [My Copy] Nature Reviews Genetics, Vol. 6, No. 5. (01 May 2005), pp. 361-375. by Frederic Delsuc, Henner Brinkmann, Herve Philippe posted to tree these phylogeny by calderonv on 2009-11-05 11:43:13 as along with 11 people pablocarb stharward adampah michaelbarton treangen fhsantanna druvus maximilianh cmzmasek gjuggler dmc
	Assessment of phylogenomic and orthology approaches for phylogenetic inference [My Copy] Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 815-824. by B. E. Dutilh, V. van Noort, R. T. J. M. van der Heijden, T. Boekhout, B. Snel, M. A. Huynen posted to these phylogeny by calderonv on 2009-11-05 11:38:59 as along with 3 people and 1 group skembel maximilianh svdate iSEEM
	Weighting, Partitioning, and Combining Characters in Phylogenetic Analysis [My Copy] Systematic Biology, Vol. 43, No. 2. (1994), pp. 278-287. by Paul T. Chippindale, John J. Wiens posted to these phylogeny by calderonv on 2009-11-05 11:35:06 as
	The evolution of supertrees [My Copy] Trends in Ecology & Evolution, Vol. 19, No. 6. (June 2004), pp. 315-322. by O. Binindaemonds posted to these supertree phylogeny by calderonv on 2009-11-05 11:31:42 as
	Phylogenomics: the beginning of incongruence? [My Copy] Trends in Genetics, Vol. 22, No. 4. (18 April 2006), pp. 225-231. by O. Jeffroy, H. Brinkmann, F. Delsuc, H. Philippe posted to these phylogeny by calderonv on 2009-11-05 11:29:41 as along with 5 people and 4 groups aprasad indigoviolet dchughes taka kinestetika EisenLab G4ID microbiology_nijmegen Genetics-of-Gambling
	Evolutionary history of trypanosomes from South American caiman ( Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes [My Copy] Parasitology, Vol. 136, No. 01. (2009), pp. 55-65. by L. B. Viola, R. S. Almeida, R. C. Ferreira, et al.M. Campaner, C. S. A. Takata, A. C. Rodrigues, F. Paiva, E. P. Camargo, M. M. G. Teixeira posted to trypanosoma ribosomal-gene phylogeography phylogeny ggapdh-gene evolution caiman-yacare by alokdixit7 on 2009-11-05 05:34:32 as
	Phylogeny of prokaryotes: does it exist and why should we care? [My Copy] Research in Microbiology, Vol. 160, No. 7. (23 September 2009), pp. 513-521. by Simonetta Gribaldo, Celine Brochier posted to these phylogeny evolution by calderonv on 2009-11-04 17:54:51 as
	Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 44. (3 November 2009), pp. 18621-18626. by W. John Kress, David L. Erickson, F. Andrew Jones, et al.Nathan G. Swenson, Rolando Perez, Oris Sanjur, Eldredge Bermingham posted to woody_trees sequence_data phylogeny natural_communities molecular_phylogenies forest_dynamics dna_barcode community_ecology barcodes by tkeitt on 2009-11-04 15:50:41 as along with 1 person dchughes
	Five Questions about Microsporidia [My Copy] PLoS Pathog, Vol. 5, No. 9. (25 September 2009), e1000489. by Patrick Keeling posted to phylogeny microsporidia history fungi by fungal on 2009-11-04 15:07:13 as along with 2 people and 1 group bcondon stajich Mycology
	Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 44. (3 November 2009), pp. 18644-18649. by Jared E. Decker, J. Chris Pires, Gavin C. Conant, et al.Stephanie D. McKay, Michael P. Heaton, Kefei Chen, Alan Cooper, Johanna Vilkki, Christopher M. Seabury, Alexandre R. Caetano, Gary S. Johnson, Rick A. Brenneman, Olivier Hanotte, Lori S. Eggert, Pamela Wiener, Jong-Joo Kim, Kwan S. Kim, Tad S. Sonstegard, Curt P. Van Tassell, Holly L. Neibergs, John C. McEwan, Rudiger Brauning, Luiz L. Coutinho, Masroor E. Babar, Gregory A. Wilson, Matthew C. McClure, Megan M. Rolf, JaeWoo Kim, Robert D. Schnabel, Jeremy F. Taylor posted to phylogeny phylogenomics molecular-phylogenetics by dchughes on 2009-11-03 22:50:55 as
	Protein phylogenies provide evidence of a radical discontinuity between arthropod and vertebrate immune systems [My Copy] Immunogenetics, Vol. 47, No. 4. (16 February 1998), pp. 283-296. by A. L. Hughes posted to vertebrate phylogeny immune homology evolution arthropod adaptve_immune_system adaptive_immune_system by tomhebbron on 2009-11-03 15:18:22 as
	Animal evolution. The end of the intermediate taxa? [My Copy] Trends Genet, Vol. 15, No. 3. (March 1999), pp. 104-108. by A. Adoutte, G. Balavoine, N. Lartillot, R. de Rosa posted to phylogeny evolution development by aaltenburger on 2009-11-03 09:09:04 as along with 4 people timflutre altotor hervelequere tanchize
	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 phylogeny bayesian by carpi on 2009-11-02 16:43:03 as along with 3 people druvus ryanraaum cstrasser
	Discovering the Phylodynamics of RNA Viruses [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (26 October 2009), e1000505. by Edward C. Holmes, Bryan T. Grenfell posted to phylogeny evolution epidemology by kshameer on 2009-10-31 07:41:20 as along with 1 person friendpine
	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 xml_language phylogeny by kshameer on 2009-10-30 06:52:59 as along with 6 people and 1 group operon cisevol Geknitics druvus phoenixzxl cmzmasek BergmanLab
	DIVERGENCE OF MITOCHONDRIAL DNA IS NOT CORROBORATED BY NUCLEAR DNA, MORPHOLOGY, OR BEHAVIOR IN DROSOPHILA SIMULANS [My Copy] Evolution, Vol. 56, No. 3. (2002), pp. 527-545. by William, Barry Chernoff, Avis C. James posted to wolbachia phylogeography phylogeny mitochondrial_genome mitochondrial_genes mitochondrial_dna mitochondria by lizbiogen on 2009-10-29 16:35:51 as
	Polyphyly of the Zaprionus genus group (Diptera: Drosophilidae) [My Copy] Molecular Phylogenetics and Evolution (15 September 2009) by Amir Yassin, Jean-Luc Da Lage, Jean R. David, et al.Masanori Kondo, Lilian Madi-Ravazzi, Stéphane R. Prigent, Masanori J. Toda posted to zaprionus samoaia phylogeny phorticella drosophilidae by lizbiogen on 2009-10-28 19:38:49 as along with 1 person gwallau
	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 phylogeny network co-regulated by druvus on 2009-10-28 16:54:07 as along with 2 people and 1 group CLH_1865 stajich Mycology
	Ancient DNA resolves identity and phylogeny of New Zealand's extinct and living quail (Coturnix sp.). [My Copy] PloS one, Vol. 4, No. 7. (28 July 2009), e6400. by Mark Seabrook-Davison, Leon Huynen, David M. Lambert, Dianne H. Brunton posted to phylogeny forensic bird avian ancient-dna by dchughes on 2009-10-28 11:46:31 as along with 1 person neils
	FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1641-1650. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted to trees taxonomy raxml phylogeny bootstrap bioinformatics by pyilmaz on 2009-10-27 21:43:18 as along with 8 people and 2 groups druvus houniao007 rneches djkt ppgardne jwm skembel nuin iSEEM Journal picks
	Nucleic acid techniques in bacterial systematics and identification. [My Copy] International journal of food microbiology, Vol. 120, No. 3. (15 December 2007), pp. 225-236. by Wolfgang Ludwig posted to taxonomy phylogeny by pyilmaz on 2009-10-26 22:05:10 as
	Shifting the genomic gold standard for the prokaryotic species definition [My Copy] Proceedings of the National Academy of Sciences (23 October 2009) by Michael Richter, Ramon RossellÃ³-MÃ³ra posted to tetranucleotides taxonomy phylogeny bioinformatics by pyilmaz on 2009-10-26 21:49:47 as along with 1 person and 1 group Katje microbiology_nijmegen
	Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion [My Copy] Nucl. Acids Res. (18 September 2009), gkp746. by Pui Y. Yung, Catherine Burke, Matt Lewis, Suhelen Egan, Staffan Kjelleberg, Torsten Thomas posted to prokariotic phylogeny microbiology metagenomics bateria by inquil on 2009-10-26 10:29:55 as along with 1 person neils
	The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits [My Copy] Syst Biol (4 June 2009), syp020. by Conrad L. Schoch, Gi-Ho Sung, Francesc Lopez-Giraldez, et al.Jeffrey P. Townsend, Jolanta Miadlikowska, Valerie Hofstetter, Barbara Robbertse, P. Brandon Matheny, Frank Kauff, Zheng Wang, Cecile Gueidan, Rachael M. Andrie, Kristin Trippe, Linda M. Ciufetti, Anja Wynns, Emily Fraker, Brendan P. Hodkinson, Gregory Bonito, Johannes Z. Groenewald, Mahdi Arzanlou, G. Sybren de Hoog, Pedro W. Crous, David Hewitt, Donald H. Pfister, Kristin Peterson, Marieka Gryzenhout, Michael J. Wingfield, Andre Aptroot, Sung-Oui Suh, Meredith Blackwell, David M. Hillis, Gareth W. Griffith, Lisa A. Castlebury, Amy Y. Rossman, H. Thorsten Lumbsch, Robert Lucking, Burkhard Budel, Alexandra Rauhut, Paul Diederich, Damien Ertz, David M. Geiser, Kentaro Hosaka, Patrik Inderbitzin, Jan Kohlmeyer, Brigitte Volkmann-Kohlmeyer, Lizel Mostert, O'Donnell Kerry, Harrie Sipman, Jack D. Rogers, Robert A. Shoemaker, Junta Sugiyama, Richard C. Summerbell, Wendy Untereiner, Peter R. Johnston, Soili Stenroos, Alga Zuccaro, Paul S. Dyer, Peter D. Crittenden, Mariette S. Cole, Karen Hansen, James M. Trappe, Rebecca Yahr, Francois Lutzoni, Joseph W. Spatafora posted to phylogeny ascomycota by fungal on 2009-10-23 02:33:26 as
	Separating the determinants of phylogenetic community structure [My Copy] Ecology Letters, Vol. 10, No. 10. (October 2007), pp. 917-925. by Matthew R. Helmus, Kristina Savage, Matthew W. Diebel, Jeffrey T. Maxted, Anthony R. Ives posted to phylogeny diversity community_structure by ltitodem on 2009-10-22 20:06:06 as along with 1 person russelld
	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 phylogeny mammalian_genomes evolutionary_history by Geknitics on 2009-10-22 16:21:05 as along with 7 people djkt wendygarnica jsatkosk mkiyer antariksh sujaikumar bpcusack
	A phylogeny of Drosophilidae using the <i>Amyrel</i> gene: questioning the <i>Drosophila melanogaster</i> species group boundaries [My Copy] Journal of Zoological Systematics and Evolutionary Research, Vol. 45, No. 1. (February 2007), pp. 47-63. by J. L. Da Lage, G. J. Kergoat, F. Maczkowiak, J. F. Silvain, M. L. Cariou, D. Lachaise posted to phylogeny drosophilidae amyrel by lizbiogen on 2009-10-22 13:55:10 as along with 1 person gwallau
	The potential and peril of the supertree approach: A response to van der Linde and Houle [My Copy] Insect Systematics & Evolution (2008), pp. 269-280. by Patrick M. O'Grady, Richard T. Lapoint, Gordon M. Bennett posted to supertree phylogeny drosophilidae by lizbiogen on 2009-10-21 22:30:40 as
	Response to O'Grady et al.: The potential and peril of the supertree approach [My Copy] Insect Systematics & Evolution (2008), pp. 281-286. by Kim van der Linde, David Houle posted to supertree phylogeny drosophilidae by lizbiogen on 2009-10-21 22:27:48 as

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evolution	380
plant	119
bioinformatics	93
software	93
alignment	88
genome	73
diversity	72
phylogenomics	68
comparative	60
methods	60
phylogenetics	57
reconstruction	56
statistics	55
taxonomy	53
islands	49
review	49
tree	46
bacteria	44
bayesian	44
celegans	41
elegans	41
article	40
c_elegans	40
caenorhabditis_elegans	40
likelihood	40
nematode	40
sequence	40
wormbase	40
contrasts	38
biogeography	36
algorithms	34
genetics	34
method	34
fungi	33
protein_sequence	32
genomics	31
inference	30
protein	30
comparative_genomics	29
its	28
phyloinformatics	28
algorithm	27
gene	27
molecular	27
clock-like	26
substitution-models	26
molecular_sequence_data	24
orthology	24
cpdna	23
drosophila	23
hgt	23
model	23
classification	22
accuracy	21
diversification	21
sequence_comparison	21
these	21
16s	20
amino_acid_sequence	20
data-mining	20
metagenomics	19
network	19
prediction	18
selection	18
supertree	18
canary	17
divergence	17
population-genetics	17
speciation	17
base_sequence	16
distance	16
dna	16
evolutionary-genomics	16
morphology	16
protists	16
adaptive-radiation	15
choanoflagellates	15
culture	15
models	15
ratio-test	15
human	14
2007	13
ecology	13
family	13
have_as_pdf	13
history	13
marine	13
protein_evolution	13
sequence_alignment	13
systematics	13
biodiversity	12
caenorhabditis_elegans_genetics	12
database	12
francisella	12
homology	12
microbial-ecology	12
microeukaryotes	12
networks	12
prokaryotes	12
proteome	12

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