Tag substitution-models [37 articles] Export

Recent papers classified by the tag substitution-models.

	Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection [My Copy] Mol Biol Evol, Vol. 22, No. 5. (1 May 2005), pp. 1208-1222. by Sergei L. Kosakovsky Pond, Simon D. W. Frost posted to substitution-models selection reconstruction rates models methods likelihood estimation bayesian alignment by rvosa to the group FAB-lab on 2009-12-02 16:32:19 as along with 6 people druvus operon BioNica Garamonfok marck gjuggler
	HyPhy: hypothesis testing using phylogenies [My Copy] Bioinformatics, Vol. 21, No. 5. (1 March 2005), pp. 676-679. by Sergei L. Pond, Simon D. W. Frost, Spencer V. Muse posted to substitution-models statistics software reconstruction ratio-test programming phyloinformatics models methods likelihood inference estimation data-mining alignment algorithms by rvosa to the group FAB-lab on 2009-12-02 16:28:42 as along with 6 people BioNica druvus operon radek Natasha Garamonfok
	Reliabilities of identifying positive selection by the branch-site and the site-prediction methods [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6700-6705. by Masafumi Nozawa, Yoshiyuki Suzuki, Masatoshi Nei posted to adaptation amino-acid likelihood methods protein selection substitution-models vertebrates by rvosa to the group FAB-lab on 2009-04-24 09:15:52 as along with 8 people ckenaley sameersoi djkt ramiro2k gjuggler bpcusack atphan gulsacan
	Datamonkey: rapid detection of selective pressure on individual sites of codon alignments [My Copy] Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2531-2533. by Sergei L. K. Pond, Simon D. Frost posted to data-mining selection sequence-evolution software substitution-models by rvosa to the group FAB-lab on 2008-08-14 00:43:38 as along with 2 people druvus BioNica
	Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid–cercopithecoid divergence [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 49. (7 December 2004), pp. 17021-17026. by Michael E. Steiper, Nathan M. Young, Tika Y. Sukarna posted to animals cercopithecidae cercopithecinae clock-like dna fossils hominidae mammals primates rates substitution-models by rvosa to the group FAB-lab on 2008-08-12 07:49:38 as
	Forces Shaping the Fastest Evolving Regions in the Human Genome [My Copy] PLoS Genet, Vol. 2, No. 10. (13 October 2006), e168. by Katherine S. Pollard, Sofie R. Salama, Bryan King, et al.Andrew D. Kern, Tim Dreszer, Sol Katzman, Adam Siepel, Jakob S. Pedersen, Gill Bejerano, Robert Baertsch, Kate R. Rosenbloom, Jim Kent, David Haussler posted to animals divergence dna evolution genome hominidae humans mammals rates substitution-models by rvosa to the group FAB-lab on 2008-08-12 04:13:38 as along with 6 people and 1 group balicea sriesenfeld skembel eskay nickluscombe iris42 EBI-regulation
	Frequent false detection of positive selection by the likelihood method with branch-site models. [My Copy] Molecular biology and evolution, Vol. 21, No. 7. (1 July 2004), pp. 1332-1339. by Jianzhi Zhang posted to genetics likelihood methods selection sequence-evolution substitution-models by rvosa to the group FAB-lab on 2008-08-12 04:02:24 as along with 2 people BioNica Garamonfok
	Molecular evolution of human visual pigment genes. [My Copy] Molecular biology and evolution, Vol. 6, No. 2. (March 1989), pp. 186-197. by S. Yokoyama, R. Yokoyama posted to evolution humans sequence-evolution substitution-models vision by rvosa to the group FAB-lab on 2008-08-10 08:06:00 as
	Is the population size of a species relevant to its evolution? [My Copy] Evolution Int J Org Evolution, Vol. 55, No. 11. (11 November 2001), pp. 2161-2169. by J. H. Gillespie posted to population-genetics rates selection substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:56:15 as along with 4 people haloin aprasad jmeppley bpcusack
	Metabolic rate does not calibrate the molecular clock [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15388-15393. by Robert Lanfear, Jessica A. Thomas, John J. Welch, Thomas Brey, Lindell Bromham posted to clock-like comparative morphometrics rates substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:48:24 as along with 3 people and 1 group operon Katje Borelli microbiology_nijmegen
	Calculating independent contrasts for the comparative study of substitution rates. [My Copy] Journal of theoretical biology, Vol. 251, No. 4. (21 April 2008), pp. 667-678. by J. J. Welch, D. Waxman posted to comparative contrasts likelihood methods rates substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:42:43 as along with 1 person druvus
	Strong Variations of Mitochondrial Mutation Rate across Mammals--the Longevity Hypothesis [My Copy] Mol Biol Evol, Vol. 25, No. 1. (1 January 2008), pp. 120-130. by Benoit Nabholz, Sylvain Glemin, Nicolas Galtier posted to animals clock-like comparative life-history mammals mitochondrial nuclear population-genetics rates substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:35:08 as along with 5 people operon aprasad renatomilani smbe2008 stevanspringer
	The rate of DNA evolution: effects of body size and temperature on the molecular clock. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 1. (4 January 2005), pp. 140-145. by J. F. Gillooly, A. P. Allen, G. B. West, J. H. Brown posted to clock-like comparative genome mitochondrial morphometrics nuclear rates substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:12:36 as along with 1 person timflutre
	Lineage-specific evolutionary rate in mammalian mtDNA. [My Copy] Molecular biology and evolution, Vol. 17, No. 7. (July 2000), pp. 1022-1031. by C. Gissi, A. Reyes, G. Pesole, C. Saccone posted to animals comparative genome mammals mitochondrial morphometrics rates substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:10:34 as
	Partitioning the variation in mammalian substitution rates. [My Copy] Mol Biol Evol, Vol. 20, No. 1. (January 2003), pp. 10-17. by N. G. Smith, A. Eyre-Walker posted to animals mammals mitochondrial nuclear rates sequence-evolution substitution-models by rvosa to the group FAB-lab on 2008-08-09 21:07:32 as along with 1 person mdimmic
	Correlates of substitution rate variation in mammalian protein-coding sequences. [My Copy] BMC evolutionary biology, Vol. 8 (19 February 2008), 53. by John J. Welch, Olaf R. Bininda-Emonds, Lindell Bromham posted to animals clock-like comparative divergence life-history mammals rates substitution-models by rvosa to the group FAB-lab on 2008-08-09 20:49:44 as along with 1 person gjuggler
	Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level [My Copy] Science, Vol. 314, No. 5796. (6 October 2006), pp. 119-121. by Mark Pagel, Chris Venditti, Andrew Meade posted to clock-like divergence dna evolution phylogeny rates speciation substitution-models by rvosa to the group FAB-lab on 2008-08-09 11:44:51 as along with 5 people and 1 group vtraag knaseanka brant bpcusack shikin EisenLab
	Phylogenetic Mixture Models Can Reduce Node-Density Artifacts [My Copy] Systematic Biology, Vol. 57, No. 2. (2008), pp. 286-293. by Chris Venditti, Andrew Meade, Mark Pagel posted to inference methods models phylogeny sequence-evolution substitution-models by rvosa to the group FAB-lab on 2008-08-09 10:43:23 as along with 1 person aprasad
	A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data [My Copy] Syst Biol, Vol. 53, No. 4. (1 August 2004), pp. 571-581. by Mark Pagel, Andrew Meade posted to characters genetics methods models phylogeny sequence substitution-models by rvosa to the group FAB-lab on 2008-08-09 10:21:04 as along with 1 person djohnson
	The role of immunochemical differences in the phyletic development of human behavior. [My Copy] Human biology; an international record of research, Vol. 33 (May 1961), pp. 131-162. by M. Goodman posted to rates sequence-evolution substitution-models by rvosa on 2008-08-09 06:05:11 as
	An evaluation of the molecular clock hypothesis using mammalian DNA sequences [My Copy] Journal of Molecular Evolution, Vol. 25, No. 4. (1987), pp. 330-342. by Wen-Hsiung Li, Masako Tanimura, Paul Sharp posted to alignment animals dna evolution genetics primates rodents sequence-evolution substitution-models by rvosa to the group FAB-lab on 2008-08-09 05:56:41 as
	Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. [My Copy] Mol Biol Evol, Vol. 21, No. 3. (March 2004), pp. 468-488. by A. Siepel, D. Haussler posted to substitution-models by uwe on 2007-11-30 19:05:26 as along with 6 people mgledi sriesenfeld mdimmic penka djkt tale
	The Problem of Rooting Rapid Radiations [My Copy] Mol Biol Evol, Vol. 24, No. 11. (1 November 2007), pp. 2400-2411. by Liat Shavit, David Penny, Michael D. Hendy, Barbara R. Holland posted to adaptation diversification likelihood parsimony phylogeny radiation substitution-models by rvosa to the group FAB-lab on 2007-11-28 02:49:08 as
	Detecting the Node-Density Artifact in Phylogeny Reconstruction [My Copy] Systematic Biology, Vol. 55, No. 4. (August 2006), pp. 637-643. by Chris Venditti, Andrew Meade, Mark Pagel posted to algorithms clock-like divergence diversification inference likelihood phylogeny reconstruction substitution-models by rvosa on 2007-11-20 02:29:50 as
	The likelihood node density effect and consequences for evolutionary studies of molecular rates [My Copy] Evolution, Vol. 61, No. 10., pp. 2293-2307. by Andrew F. Hugall, Michael S. Lee posted to bayesian divergence likelihood phylogeny reconstruction substitution-models by rvosa on 2007-11-20 00:54:26 as
	On the overdispersed molecular clock. [My Copy] Genetics, Vol. 116, No. 1. (May 1987), pp. 169-179. by N. Takahata posted to clock-like likelihood phylogeny ratio-test selection statistics substitution-models by rvosa on 2007-11-19 22:05:08 as along with 1 person mdimmic
	Maximum Likelihood Trees from DNA Sequences: A Peculiar Statistical Estimation Problem [My Copy] Systematic Biology, Vol. 44, No. 3. (1995), pp. 384-399. by Ziheng Yang, Nick Goldman, Adrian Friday posted to clock-like inference likelihood phylogeny ratio-test statistics substitution-models by rvosa on 2007-11-19 21:52:03 as
	The delayed rise of present-day mammals [My Copy] Nature, Vol. 446, No. 7135. (2007), pp. 507-512. by Olaf R. P. Bininda-Emonds, Marcel Cardillo, Kate E. Jones, et al.Ross D. E. Macphee, Robin M. D. Beck, Richard Grenyer, Samantha A. Price, Rutger A. Vos, John L. Gittleman, Andy Purvis posted to biodiversity clock-like divergence diversification fossils phylogeny phyloinformatics primates ratio-test reconstruction substitution-models supertree by rvosa on 2007-10-13 22:04:44 as along with 5 people and 2 groups bpcusack gjuggler dchughes nurban dwildman G4ID Genetics-of-Gambling
	A composite estimate of primate phylogeny. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 348, No. 1326. (29 June 1995), pp. 405-421. by A. Purvis posted to algorithms animals biodiversity clock-like diversification fossils mammals mrp phylogeny phyloinformatics primates substitution-models supertree vertebrates by rvosa on 2007-10-13 21:47:21 as along with 2 people memerman kieran101
	Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 359, No. 1450. (29 October 2004), pp. 1477-1483. by T. J. Near, M. J. Sanderson posted to clock-like divergence fossils inference likelihood reconstruction substitution-models by rvosa to the group FAB-lab on 2005-10-13 12:58:12 as
	Maximum-Likelihood Estimation of Population Divergence Times and Population Phylogeny in Models without Mutation [My Copy] Evolution, Vol. 52, No. 3. (1998), pp. 669-677. by Rasmus Nielsen, Joanna L. Mountain, John P. Huelsenbeck, Montgomery Slatkin posted to bayesian clock-like divergence likelihood reconstruction substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:39:39 as along with 1 person jmeppley
	Temporal scaling of molecular evolution in primates and other mammals. [My Copy] Mol Biol Evol, Vol. 3, No. 3. (May 1986), pp. 205-221. by P. D. Gingerich posted to clock-like comparative divergence phylogeny reconstruction substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:28:42 as
	Recombination and the molecular clock. [My Copy] Mol Biol Evol, Vol. 17, No. 10. (October 2000), pp. 1578-1579. by M. H. Schierup, J. Hein posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:20:48 as
	Unveiling the molecular clock in the presence of recombination. [My Copy] Mol Biol Evol, Vol. 18, No. 10. (October 2001), pp. 1976-1978. by D. Posada posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:18:32 as
	Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. [My Copy] Mol Biol Evol, Vol. 21, No. 6. (June 2004), pp. 1123-1133. by John P. Huelsenbeck, Bret Larget, Michael E. Alfaro posted to algorithms bayesian clock-like likelihood markov-chains methods monte-carlo phylogeny ratio-test substitution-models by rvosa on 2005-10-12 21:11:30 as along with 2 people and 1 group zhouyanpharm aprasad FAB-lab
	Using models of nucleotide evolution to build phylogenetic trees. [My Copy] Dev Comp Immunol, Vol. 29, No. 3. (2005), pp. 211-227. by D. H. Bos, D. Posada posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 21:10:26 as along with 1 person lizbiogen
	Maximum-Likelihood Models for Combined Analyses of Multiple Sequence Data [My Copy] J Mol Evol, Vol. 42, No. 5. (May 1996), pp. 587-596. by Z. Yang posted to clock-like likelihood phylogeny ratio-test substitution-models by rvosa to the group FAB-lab on 2005-10-12 20:41:58 as

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clock-like	33
likelihood	30
phylogeny	26
rates	26
methods	16
animals	15
divergence	15
ratio-test	15
comparative	14
mammals	13
reconstruction	13
sequence-evolution	13
selection	11
evolution	10
models	9
dna	8
inference	8
mitochondrial	8
bayesian	7
genetics	7
alignment	6
fossils	6
genome	6
morphometrics	6
nuclear	6
primates	6
algorithms	5
diversification	5
adaptation	4
data-mining	4
estimation	4
hominidae	4
humans	4
life-history	4
phyloinformatics	4
population-genetics	4
software	4
statistics	4
vertebrates	3
amino-acid	2
biodiversity	2
cercopithecidae	2
cercopithecinae	2
characters	2
contrasts	2
parsimony	2
programming	2
protein	2
radiation	2
recombination	2
rodents	2
sequence	2
speciation	2
supertree	2
vision	2
markov-chains	1
monte-carlo	1
mrp	1
rna	1
viruses	1

Tag substitution-models [37 articles] Export

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