rvosa's substitution-models [90 articles] Export

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	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 on 2009-12-02 16:32:19 as along with 6 people and 1 group druvus operon BioNica Garamonfok marck gjuggler FAB-lab
	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 on 2009-12-02 16:28:42 as along with 6 people and 1 group BioNica druvus operon radek Natasha Garamonfok FAB-lab
	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 on 2009-04-24 09:15:52 as along with 8 people and 1 group ckenaley sameersoi djkt ramiro2k gjuggler bpcusack atphan gulsacan FAB-lab
	MAXIMUM LIKELIHOOD FRAMEWORK FOR GENETIC SEQUENCE ANALYSIS [My Copy] by Sergei L. Pond posted to algorithms dna estimation inference likelihood methods models phylogeny phyloinformatics sequence-evolution substitution-models by rvosa on 2008-12-18 02:20:47 as along with 1 group FAB-lab
	Mixture models in phylogenetic inference [My Copy] In Statistical and computational challenges in molecular phylogenetics and evolution (28 April 2008) by Mark Pagel posted to bayesian markov-chains methods monte-carlo phylogeny rates substitution-models by rvosa on 2008-08-18 02:27:00 as along with 1 group FAB-lab
	Modelling Heterotachy in Phylogenetic Inference by Reversible-Jump Markov chain Monte Carlo [My Copy] Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, Vol. In review by Mark Pagel, Andrew Meade posted to bayesian markov-chains methods monte-carlo rates substitution-models by rvosa on 2008-08-18 01:50:23 as along with 1 group FAB-lab
	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 on 2008-08-14 00:43:38 as along with 2 people and 1 group druvus BioNica FAB-lab
	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 on 2008-08-12 07:49:38 as along with 1 group FAB-lab
	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 on 2008-08-12 04:13:37 as along with 6 people and 2 groups balicea sriesenfeld skembel eskay nickluscombe iris42 EBI-regulation FAB-lab
	Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models [My Copy] Mol Biol Evol, 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 on 2008-08-12 04:02:24 as along with 1 person and 1 group Garamonfok FAB-lab
	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 on 2008-08-10 08:06:00 as along with 1 group FAB-lab
	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 on 2008-08-09 21:56:15 as along with 4 people and 1 group haloin aprasad jmeppley bpcusack FAB-lab
	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 on 2008-08-09 21:48:24 as along with 3 people and 2 groups operon Katje Borelli microbiology_nijmegen FAB-lab
	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 on 2008-08-09 21:42:43 as along with 1 person and 1 group druvus FAB-lab
	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 on 2008-08-09 21:35:08 as along with 5 people and 1 group operon aprasad renatomilani smbe2008 stevanspringer FAB-lab
	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 on 2008-08-09 21:12:36 as along with 1 person and 1 group timflutre FAB-lab
	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 on 2008-08-09 21:10:34 as along with 1 group FAB-lab
	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 on 2008-08-09 21:07:32 as along with 1 person and 1 group mdimmic FAB-lab
	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. P. Bininda-Emonds, Lindell Bromham posted to animals clock-like comparative divergence life-history mammals rates substitution-models by rvosa on 2008-08-09 20:49:43 as along with 1 person and 1 group gjuggler FAB-lab
	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 on 2008-08-09 11:44:50 as along with 5 people and 2 groups vtraag knaseanka brant bpcusack shikin EisenLab FAB-lab
	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 on 2008-08-09 10:43:22 as along with 1 person and 1 group aprasad FAB-lab
	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 on 2008-08-09 10:21:04 as along with 1 person and 1 group djohnson FAB-lab
	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 on 2008-08-09 05:56:40 as along with 1 group FAB-lab
	Fast Genes and Slow Clades: Comparative Rates of Molecular Evolution in Mammals [My Copy] Evolutionary Bioinformatics, Vol. 3 (2007), pp. 59-85. by Olaf R. P. Bininda-Emonds posted to animals clock-like data-mining databases mammals rates sequence-evolution substitution-models supertree by rvosa on 2008-08-08 08:22:08 as
	Accelerated molecular evolution as a consequence of transitions to mutualism [My Copy] Proceedings of the national academy of sciences, Vol. 94, No. 21. (1997), pp. 11422-11427. by Francois Lutzoni, Mark Pagel posted to bacteria comparative divergence fungi methods rates ratio-test substitution-models by rvosa on 2008-07-11 18:54:57 as along with 1 group FAB-lab
	Estimating Evolutionary Rates in the Primate epsilon-globin Pseudogene [My Copy] (12 August 2004) by Toby Johnson posted to animals likelihood mammals methods primates rates ratio-test software substitution-models vertebrates by rvosa on 2008-02-08 03:13:21 as along with 1 group FAB-lab
	Molecular evolutionary dynamics of cytochrome b in Strepsirrhine primates: the phylogenetic significance of third-position transversions [My Copy] Molecular Biology and Evolution, Vol. 13 (1996), pp. 1339-1350. by A. D. Yoder, R. Vilgalys, Maryellen Ruvolo posted to animals mammals mitochondrial primates sequence-evolution strepsirrhines substitution-models vertebrates by rvosa on 2008-02-07 00:05:53 as
	Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species [My Copy] Systematic Biology, Vol. 52, No. 5. (2003), pp. 705-716. by Z. H. Yang, A. D. Yoder posted to animals bayesian clock-like divergence lemuridae likelihood mammals markov-chains monte-carlo morphology primates rates substitution-models vertebrates by rvosa on 2008-02-07 00:05:52 as
	Estimation of the Transition/Transversion Rate Bias and Species Sampling [My Copy] Journal of Molecular Evolution, Vol. 48, No. 3. (March 1999), pp. 274-283. by Ziheng Yang, A. D. Yoder posted to animals likelihood mammals primates source-trees substitution-models vertebrates by rvosa on 2008-02-07 00:05:52 as
	Bayesian Phylogenetic Inference Using DNA Sequences: A Markov Chain Monte Carlo Method [My Copy] Molecular Biology and Evolution, Vol. 14, No. 7. (1997), pp. 717-724. by Ziheng Yang, Bruce Rannala posted to bayesian diversification extinction markov-chains monte-carlo phylogeny speciation substitution-models by rvosa on 2008-02-07 00:05:52 as
	Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution [My Copy] Molecular Biology and Evolution, Vol. 15, No. 5. (1998), pp. 568-573. by Ziheng Yang posted to animals likelihood mammals primates protein ratio-test selection substitution-models vertebrates by rvosa on 2008-02-07 00:05:52 as
	PAML: a program package for phylogenetic analysis by maximum likelihood [My Copy] CABIOS, Vol. 13 (1997), pp. 555-556. by Ziheng Yang posted to likelihood software substitution-models by rvosa on 2008-02-07 00:05:52 as
	Molecular Evolution of Cytochrome c Oxidase Subunit I in Primates: Is There Coevolution between Mitochondrial and Nuclear Genomes? [My Copy] Molecular Phylogenetics and Evolution, Vol. 17, No. 2. (January 2000), pp. 294-304. by Wei Wu, T. R. Schmidt, M. Goodman, Lawrence I. Grossman posted to animals dna genome mammals mitochondrial nuclear phylogenomics primates source-trees substitution-models vertebrates by rvosa on 2008-02-07 00:05:52 as
	Molecular Evolution of Cytochrome c Oxidase Subunit IV: Evidence for Positive Selection in Simian Primates [My Copy] Journal of Molecular Evolution, Vol. 44, No. 5. (May 1997), pp. 477-491. by Wei Wu, M. Goodman, Margaret I. Lomax, Lawrence I. Grossman posted to animals dna mammals mitochondrial primates rates selection source-trees substitution-models vertebrates by rvosa on 2008-02-07 00:05:52 as
	Comparison between phylogeny of introns and exons in primates [My Copy] Chinese Science Bulletin, Vol. 44, No. 21. (1999), pp. 1940-1946. by N. Wang, R. Chen posted to animals evolution inference mammals phylogeny primates sequence-evolution substitution-models vertebrates by rvosa on 2008-02-07 00:05:51 as
	Inching toward Reality: An Improved Likelihood Model of Sequence Evolution [My Copy] Journal of Molecular Evolution, Vol. 34 (1992), pp. 3-16. by Jeffrey L. Thorne, Hirohisa Kishino, Joseph Felsenstein posted to algorithms alignment evolution likelihood methods programming substitution-models by rvosa on 2008-02-07 00:05:50 as
	Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees [My Copy] Molecular Biology and Evolution, Vol. 10 (1993), pp. 512-526. by K. Tamura, M. Nei posted to animals hominidae mammals mitochondrial primates sequence-evolution substitution-models vertebrates by rvosa on 2008-02-07 00:05:49 as
	Molecular Phylogeny of the New World Monkeys (Platyrrhini, Primates) Based on Two Unlinked Nuclear Genes: IRBP Intron 1 and e-Globin Sequences [My Copy] American Journal of Physical Anthropology, Vol. 100 (1996), pp. 153-179. by Horacio Schneider, Iracilda Sampaio, M. L. Harada, et al.C. M. L. Barroso, Maria, John Czelusniak, M. Goodman posted to animals cebidae evolution genetics mammals parsimony primates sequence-evolution source-trees substitution-models vertebrates by rvosa on 2008-02-07 00:05:46 as
	Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of Primates [My Copy] Molecular Biology and Evolution, Vol. 11, No. 3. (1994), pp. 504-512. by N. Saitou, S. Ueda posted to animals mammals primates rates sequence-evolution substitution-models vertebrates by rvosa on 2008-02-07 00:05:45 as
	Estimating divergence dates from molecular sequences [My Copy] Molecular Biology and Evolution, Vol. 15, No. 4. (1998), pp. 442-448. by A. Rambaut, L. Bromham posted to animals birds clock-like divergence dna evolution fossils likelihood mammals methods mitochondrial phylogeny rates sequence substitution-models vertebrates by rvosa on 2008-02-07 00:05:43 as
	Sampling strategies for delimiting species: Genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata : Liolaemidae) in Andean-Patagonian South America [My Copy] Systematic Biology, Vol. 52, No. 2. (2003), pp. 159-185. by M. Morando, L. J. Avila, J. W. Sites posted to animals biodiversity biogeography data-mining evolution lizards methods phyloinformatics population population-genetics regions speciation substitution-models taxonomy vertebrates by rvosa on 2008-02-07 00:05:38 as
	Performance-based selection of likelihood models for phylogeny estimation [My Copy] Systematic Biology, Vol. 52, No. 5. (2003), pp. 674-683. by V. Minin, Z. Abdo, P. Joyce, J. Sullivan posted to bayesian likelihood phylogeny ratio-test substitution-models by rvosa on 2008-02-07 00:05:37 as
	Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation [My Copy] BMC Evolutionary Biology, Vol. 5, No. 8. (2005) by Jessica C. Mar, Timothy J. Harlow, Mark A. Ragan posted to bayesian likelihood phylogeny protein substitution-models by rvosa on 2008-02-07 00:05:36 as
	Out of Africa: molecular phylogenetics and biogeography of Wolffiella (Lemnaceae) [My Copy] Biological Journal of the Linnean Society, Vol. 79, No. 4. (2003), pp. 565-576. by R. T. Kimball, D. J. Crawford, D. H. Les, E. Landolt posted to biogeography classification data-mining morphology plants substitution-models taxonomy by rvosa on 2008-02-07 00:05:33 as
	Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion (Odonata : Coenagrionidae) [My Copy] Systematic Biology, Vol. 52, No. 1. (2003), pp. 89-109. by S. Jordan, C. Simon, D. Polhemus posted to adaptation animals bayesian insects invertebrates likelihood mitochondrial nuclear phylogeny radiation ratio-test speciation substitution-models topology by rvosa on 2008-02-07 00:05:33 as
	When do parasites fail to speciate in response to host speciation? [My Copy] Systematic Biology, Vol. 52, No. 1. (2003), pp. 37-47. by K. P. Johnson, R. J. Adams, R. D. M. Page, D. H. Clayton posted to animals birds dna insects invertebrates mitochondrial nuclear parasitism phylogeny population-genetics rates speciation substitution-models topology vertebrates by rvosa on 2008-02-07 00:05:32 as
	Outgroup misplacement and phylogenetic inaccuracy under a molecular clock - A simulation study [My Copy] Systematic Biology, Vol. 52, No. 2. (2003), pp. 229-238. by B. R. Holland, D. Penny, M. D. Hendy posted to clock-like likelihood parsimony phenetics simulation substitution-models by rvosa on 2008-02-07 00:05:31 as
	Success of Maximum Likelihood Phylogeny Inference in the Four-Taxon Case [My Copy] Molecular Biology and Evolution, Vol. 12, No. 1. (1995), pp. 152-162. by Brandon S. Gaut, Paul O. Lewis posted to likelihood phylogeny ratio-test substitution-models by rvosa on 2008-02-07 00:05:18 as
	Inferring Pattern and Process: Maximum-Likelihood Implementation of a Nonhomogeneous Model of DNA Sequence Evolution for Phylogenetic Analysis [My Copy] Molecular Biology and Evolution, Vol. 15, No. 7. (1998), pp. 871-879. by Nicolas Galtier, Manolo Gouy posted to genetics likelihood phylogeny sequence-evolution substitution-models by rvosa on 2008-02-07 00:05:17 as

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animals	606
vertebrates	463
mammals	447
phylogeny	434
primates	422
methods	235
evolution	235
source-trees	125
dna	125
genetics	118
algorithms	116
mitochondrial	105
comparative	103
likelihood	93
rates	91
data-mining	90
substitution-models	90
speciation	89
divergence	85
invertebrates	85
morphology	82
behaviour	80
classification	80
phyloinformatics	80
biodiversity	77
diversification	76
software	76
sequence-evolution	74
humans	73
clock-like	68
insects	68
programming	65
reconstruction	64
encephalization	62
ecology	58
hominidae	58
genome	57
sequence	57
taxonomy	57
fossils	55
selection	55
models	54
bayesian	52
adaptation	51
parsimony	51
topology	49
biogeography	49
nuclear	49
parasitism	49
databases	48
dbhack1	48
protein	46
supertree	45
characters	42
sociality	40
phylogenomics	37
plants	36
sexual	36
amino-acid	33
inference	32
xml	32
markov-chains	32
monte-carlo	31
morphometrics	31
anthropology	31
extinction	29
bacteria	29
population-genetics	29
life-history	28
mrp	28
nexml	27
alignment	27
contrasts	25
ratio-test	25
karyotyping	20
population	20
lemuridae	20
radiation	20
ontology	19
simulation	19
strepsirrhines	18
rodents	18
conservation	17
statistics	16
birds	16
specialization	14
hybridization	13
viruses	13
predation	12
polymorphism	12
fungi	12
colobinae	12
homology	12
weighting	12
rna	12
networks	12
vision	11
carnivora	11
cebidae	10
graph	10
restriction	10
phenetics	9
platyrrhines	9
fishes	9
recombination	9
estimation	8
polymerase-chain-reaction	8
chiroptera	8
proteomics	7
mice	7
lexicostatistics	7
competition	7
cercopithecidae	6
regions	6
lizards	6
metabolomics	5
alcids	5
variability	5
cercopithecinae	5
cells	4
cheirogaleidae	4
rats	4
graphics	4
catarrhines	4
sine	3
haplorhini	3
cetartiodactyla	2
hylobates	2
tarsiidae	2
dogs	1
nucleic	1
philosophy	1
line	1
shrews	1
fingerprinting	1
songbirds	1
microarray	1
cattle	1

rvosa's substitution-models [90 articles] Export

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