Tag phylogeny [at least 200 articles] Export

Recent papers classified by the tag phylogeny.

	Heterotachy and long-branch attraction in phylogenetics. [My Copy] BMC evolutionary biology, Vol. 5 (2005) by Hervé Philippe, Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Frédéric Delsuc posted to statistics phylogeny modeling evolution by timflutre on 2009-11-20 15:26:12 as along with 2 people renewang rsandie
	Life History Evolution and Genome Size in Subtribe Oncidiinae (Orchidaceae) [My Copy] Ann Bot, Vol. 95, No. 1. (1 January 2005), pp. 191-199. by Mark W. Chase, Lynda Hanson, Victor A. Albert, W. Mark Whitten, Norris H. Williams posted to phylogeny orchidaceae orchid oncidiinae by tdwin1453 on 2009-11-19 17:57:59 as
	Expression pattern of the homeobox gene Not in the basal metazoan Trichoplax adhaerens. [My Copy] Gene expression patterns : GEP, Vol. 4, No. 4. (July 2004), pp. 443-447. by Cosimo Martinelli, Jürg Spring posted to sequence placozoa phylogeny not hox gene by aaltenburger on 2009-11-19 10:48:33 as
	The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2954-2956. by Victor Soria-Carrasco, Gerard Talavera, Javier Igea, Jose Castresana posted to phylogeny methods evolution bioinformatics by operon on 2009-11-19 00:07:57 as along with 3 people druvus renewang ryanraaum
	The Rutland <i>Cetiosaurus</i>: the anatomy and relationships of a Middle Jurassic British sauropod dinosaur [My Copy] Palaeontology, Vol. 45, No. 6. (2002), pp. 1049-1074. by Paul Upchurch, John Martin posted to phylogeny neural_spine cetiosaurus cervical_vertebra by martydaniel to the group Sauropod Dinosaurs on 2009-11-18 18:23:54 as along with 1 group Dinosaurs
	Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history [My Copy] Ecology Letters, Vol. 9999, No. 9999. (2009) by Marc W. Cadotte, T. Jonathan Davies, James Regetz, Steven W. Kembel, Elsa Cleland, Todd H. Oakley posted to species_richness phylogeny metrics ecological_communities community abundance by timothee-poisot on 2009-11-16 19:50:20 as along with 1 person iBartomeus
	Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within Opisthokonta [My Copy] Mol Biol Evol, Vol. 26, No. 12. (1 December 2009), pp. 2699-2709. by Matthew W. Brown, Frederick W. Spiegel, Jeffrey D. Silberman posted to phylogeny opisthokont multicellularity multicellular by stajich to the group Mycology on 2009-11-16 06:53:45 as along with 1 person protist
	Myogenesis in the basal bilaterian Symsagittifera roscoffensis (Acoela) [My Copy] Frontiers in Zoology, Vol. 5 (19 September 2008), 14. by Henrike Semmler, Xavier Bailly, Andreas Wanninger posted to phylogeny acoela by aaltenburger on 2009-11-13 13:12:15 as
	Taxonomy and molecular phylogeny of the Asian <i>Paraleucophenga</i> Hendel (Diptera, Drosophilidae) [My Copy] Zoological Journal of the Linnean Society, Vol. 155, No. 3. (2009), pp. 615-629. by O. Feng Zha, O. Jian-Jun Ga, N. Hong-Wei Che posted to phylogeny paraleucophenga morphological_key morphological_data by lizbiogen on 2009-11-12 18:51:44 as
	Evolution of genes and genomes on the Drosophila phylogeny [My Copy] Nature, Vol. 450, No. 7167. (08 November 2007), pp. 203-218. posted to phylogeny genome evolution drosophila comparative_genomics by biomcgary on 2009-11-12 17:20:51 as along with 36 people and 5 groups nuttpo daveGerrard Anachff GustavoLacerda mqbphcw3 rpetrenko gwallau chica jlncdr aprasad gjuggler lizbiogen jbsaltz druvus pradiptaray pengchy operon tmmurali indigoviolet djkt timflutre stajich zwang Garamonfok lp2 CharlesM hpaces caseybrown emptyhb urgi noor PetrovLab isimpson balicea cisevol hdopazo Bioinformatics EisenLab Mycology BergmanLab Drosophila-Genetics-Genomics-2008
	Phylo-evo-devo: combining phylogenetics with evolutionary developmental biology [My Copy] BMC Biology, Vol. 7, No. 1. (2009), 36. by Alessandro Minelli posted to phylogeny evolution evo-devo by aaltenburger on 2009-11-11 21:05:00 as along with 2 people cmzmasek cisevol
	A molecular evolutionary framework for the phylum Nematoda [My Copy] Nature, Vol. 392, No. 6671. (05 March 1998), pp. 71-75. by Mark L. Blaxter, Paul De Ley, James R. Garey, et al.Leo X. Liu, Patsy Scheldeman, Andy Vierstraete, Jacques R. Vanfleteren, Laura Y. Mackey, Mark Dorris, Linda M. Frisse, J. T. Vida, W. Kelley Thomas posted to tree-of-life phylogeny nematodes nematode_phylogeny by cmzmasek on 2009-11-11 20:22:37 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Windshield splatter analysis with the Galaxy metagenomic pipeline [My Copy] Genome Research, Vol. 19, No. 11. (9 November 2009), pp. 2144-2153. by Sergei Kosakovsky Pond, Samir Wadhawan, Francesca Chiaromonte, et al.Guruprasad Ananda, Wen-Yu Chung, James Taylor, Anton Nekrutenko posted to phylogeny metagenomics annotation by seb1 on 2009-11-11 17:34:08 as along with 8 people and 2 groups jmeppley Katje djkt operon neils idonaldson jgill kshameer microbiology_nijmegen iSEEM
	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 sequence_alingment phylogeny by memerman on 2009-11-11 16:13:48 as along with 29 people and 3 groups operon 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
	Pycnogonid affinities: a review [My Copy] Journal of Zoological Systematics & Evolutionary Research, Vol. 43, No. 1. (February 2005), pp. 8-21. by J. A. Dunlop, C. P. Arango posted to evolution review phylogeny by aaltenburger on 2009-11-11 12:42:24 as
	Rapid detection, classification and accurate alignment of up to a million or more related protein sequences [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1869-1875. by Andrew F. Neuwald posted to protein phylogeny multiple high-throughput alignment by davidmam on 2009-11-11 09:07:59 as along with 3 people and 3 groups robfsouza ollieredfernwork carlosjavierna Orengo Group Journal Picks Journal picks iSEEM
	PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (19 September 2009), 298. by Philippe Gouret, Julie Thompson, Pierre Pontarotti posted to software sequence-evolution protein phyloinformatics phylogeny genome evolution by rvosa to the group FAB-lab on 2009-11-11 03:43:20 as along with 5 people and 1 group nuin stajich scmelton druvus rschulz Mycology
	Models of Molecular Evolution and Phylogeny [My Copy] Genome Research, Vol. 8, No. 12. (1 December 1998), pp. 1233-1244. by Pietro LiÃ², Nick Goldman posted to review phylogeny genome-research by seb1 on 2009-11-10 14:31:58 as along with 5 people BioNica operon gjuggler hdopazo timflutre
	A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms [My Copy] PLoS Comput Biol, Vol. 3, No. 9. (14 September 2007), e176. by Erika M. Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova posted to statistics phylogeny indel human chimpanzee bioinformatics alignment by timflutre on 2009-11-10 12:58:06 as along with 4 people and 1 group Iden-J_GluR aprasad djkt cisevol cis-regulatory-evolution
	An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) [My Copy] PLoS ONE, Vol. 3, No. 7. (2 July 2008), e2566. by Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A. Eisen posted to phylogeny methods metagenome diversity 16s by Katje to the group microbiology_nijmegen on 2009-11-09 10:39:45 as along with 7 people and 3 groups AaronDarling skembel sriesenfeld druvus vaulot skato_toyaku djkt Papers recommended by the Roscoff Plankton Group Microbial-Ecology iSEEM
	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 6 people lianping 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 9 people and 3 groups martainn 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 2 people cmm 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

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evolution	388
plant	122
bioinformatics	96
software	95
alignment	91
genome	76
diversity	74
phylogenomics	68
methods	63
statistics	63
comparative	60
phylogenetics	57
reconstruction	56
taxonomy	56
review	52
islands	49
tree	46
bacteria	44
bayesian	44
celegans	41
elegans	41
sequence	41
article	40
c_elegans	40
caenorhabditis_elegans	40
likelihood	40
nematode	40
wormbase	40
contrasts	38
biogeography	36
genetics	35
algorithms	34
method	34
fungi	33
protein	33
genomics	32
protein_sequence	32
comparative_genomics	30
inference	30
phyloinformatics	30
gene	28
its	28
algorithm	27
molecular	27
clock-like	26
substitution-models	26
drosophila	24
molecular_sequence_data	24
orthology	24
cpdna	23
hgt	23
model	23
16s	22
classification	22
diversification	22
accuracy	21
sequence_comparison	21
these	21
amino_acid_sequence	20
data-mining	20
dna	20
metagenomics	20
network	19
human	18
prediction	18
selection	18
supertree	18
canary	17
divergence	17
population-genetics	17
speciation	17
base_sequence	16
distance	16
evolutionary-genomics	16
morphology	16
protists	16
adaptive-radiation	15
choanoflagellates	15
culture	15
models	15
ratio-test	15
indel	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
database	12
francisella	12
homology	12
microbial-ecology	12
microeukaryotes	12
networks	12
prokaryotes	12
proteome	12

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