rvosa's likelihood [93 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
	Pandit: a database of protein and associated nucleotide domains with inferred trees. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 12. (12 August 2003), pp. 1556-1563. by S. Whelan, P. I. de Bakker, N. Goldman posted to alignment amino-acid databases dbhack1 dna evolution homology likelihood methods models phylogenomics phylogeny phyloinformatics protein sequence by rvosa on 2008-12-18 02:07:33 as along with 1 person and 1 group mcox 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
	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
	Detecting putative orthologs. [My Copy] Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1710-1711. by D. P. Wall, H. B. Fraser, A. E. Hirsh posted to algorithms alignment databases data-mining genome likelihood methods phylogenomics phyloinformatics by rvosa on 2008-08-08 07:27:51 as along with 7 people and 3 groups cgaugain operon ana indigoviolet dquest ninch cerca structural_bioinformatics Bioinformatics EisenLab
	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
	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
	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
	IQPNNI: Moving Fast Through Tree Space and Stopping in Time [My Copy] Molecular Biology and Evolution, Vol. 21, No. 8. (2004), pp. 1565-1571. by Le S. Vinh, Arndt von Haeseler posted to algorithms likelihood methods by rvosa on 2008-02-07 00:05:51 as
	Organization and evolution of multifunctional Ca2+/CaM-dependent protein kinase genes [My Copy] Gene, Vol. 322 (2003), pp. 17-31. by Robert M. Tombes, Omar M. Faison, J. M. Turbeville posted to amino-acid evolution likelihood protein sequence-evolution by rvosa on 2008-02-07 00:05:50 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
	Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used [My Copy] Molecular Biology and Evolution, Vol. 17, No. 8. (2000), pp. 1251-1258. by K. Takahashi, M. Nei posted to algorithms likelihood methods parsimony by rvosa on 2008-02-07 00:05:49 as
	PAUP*: phylogenetic analysis using parsimony, version 4.0b10 [My Copy] (2003) by D. L. Swofford posted to dbhack1 likelihood parsimony phylogeny phyloinformatics software by rvosa on 2008-02-07 00:05:49 as
	Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models [My Copy] Molecular Biology and Evolution, Vol. 17, No. 6. (2000), pp. 875-881. by Korbinian Strimmer, Vincent Moulton posted to bayesian evolution graph likelihood markov-chains monte-carlo networks phylogeny by rvosa on 2008-02-07 00:05:48 as
	The maximum likelihood point for a phylogenetic tree is not unique [My Copy] Systematic Biology, Vol. 43 (1994), pp. 560-564. by M. A. Steel posted to likelihood methods phylogeny by rvosa on 2008-02-07 00:05:48 as
	Ancient allopolyploid speciation in geinae (Rosaceae): Evidence from nuclear granule-bound starch synthase (GBSSI) gene sequences [My Copy] Systematic Biology, Vol. 52, No. 3. (2003), pp. 374-385. by J. E. E. Smedmark, T. Eriksson, R. C. Evans, C. S. Campbell posted to characters evolution hybridization likelihood morphology nuclear phylogenomics phylogeny plants reconstruction sequence-evolution by rvosa on 2008-02-07 00:05:47 as
	Molecular phylogenetics of allodapine bees, with implications for the evolution of sociality and progressive rearing [My Copy] Systematic Biology, Vol. 52, No. 1. (2003), pp. 1-14. by M. P. Schwarz, N. J. Bull, S. J. B. Cooper posted to behaviour evolution life-history likelihood mitochondrial morphology nuclear parsimony sociality by rvosa on 2008-02-07 00:05:47 as
	Likelihood of ancestor states in adaptive radiation [My Copy] Evolution, Vol. 51, No. 6. (1997), pp. 1699-1711. by Dolph Schluter, Trevor Price, Arne Mooers, Donald Ludwig posted to adaptation evolution likelihood phylogeny radiation reconstruction specialization by rvosa on 2008-02-07 00:05:46 as
	Stochastic search strategy for estimation of maximum likelihood phylogenetic trees [My Copy] Systematic Biology, Vol. 50, No. 1. (2001), pp. 7-17. by L. A. Salter, D. K. Pearl posted to likelihood methods phylogeny by rvosa on 2008-02-07 00:05:45 as
	Complexity of the likelihood surface for a large DNA dataset [My Copy] Systematic Biology, Vol. 50, No. 6. (2001), pp. 970-978. by L. A. Salter posted to likelihood methods phylogeny by rvosa on 2008-02-07 00:05:45 as
	Multiple local maxima for likelihoods of phylogenetic trees: a simulation study. [My Copy] Molecular Biology and Evolution, Vol. 16 (1999), pp. 1079-1085. by J. Rogers, D. L. Swofford posted to likelihood methods phylogeny simulation by rvosa on 2008-02-07 00:05:44 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
	Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation [My Copy] In Biological evolution and statistical physics (2002) by M. Pagel, F. Lutzoni edited by M. Lssig, A. Valleriani posted to adaptation characters comparative evolution likelihood reconstruction by rvosa on 2008-02-07 00:05:41 as
	The maximum likelihood approach to reconstructing ancestral character states of discrete characters in phylogenies [My Copy] Systematic Biology, Vol. 48 (1999), pp. 612-622. by M. Pagel posted to characters comparative likelihood reconstruction by rvosa on 2008-02-07 00:05:41 as
	Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters [My Copy] Proceedings of the Royal Society London Series B, Vol. 255 (1994), pp. 37-45. by M. Pagel posted to characters comparative evolution likelihood methods phylogeny reconstruction by rvosa on 2008-02-07 00:05:41 as
	NJML+: An extension of the NJML method to handle protein sequence data and computer software implementation [My Copy] Molecular Biology and Evolution, Vol. 18, No. 11. (2001), pp. 1983-1992. by S. Ota, W. H. Li posted to algorithms amino-acid likelihood methods phenetics protein software by rvosa on 2008-02-07 00:05:40 as
	NJML: A hybrid algorithm for the neighbor-joining and maximum-likelihood methods [My Copy] Molecular Biology and Evolution, Vol. 17, No. 9. (2000), pp. 1401-1409. by S. Ota, W. H. Li posted to algorithms likelihood phenetics by rvosa on 2008-02-07 00:05:40 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
	Molecular systematics of cowries (Gastropoda : Cypraeidae) and diversification patterns in the tropics [My Copy] Biological Journal of the Linnean Society, Vol. 79, No. 3. (2003), pp. 401-459. by C. P. Meyer posted to biogeography classification divergence diversification extinction likelihood mitochondrial morphology phylogeny rates speciation topology 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
	The phylogeny of the subgroups within the melanogaster species group: Likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny [My Copy] Molecular Phylogenetics and Evolution, Vol. 37, No. 1. (2004), pp. 15-24. by Rebecca L. Lewis, Andrew T. Beckenbach, Arne posted to bayesian likelihood markov-chains mitochondrial monte-carlo ratio-test by rvosa on 2008-02-07 00:05:34 as
	A Genetic Algorithm for Maximum-Likelihood Phylogeny Inference Using Nucleotide Sequence Data [My Copy] Molecular Biology and Evolution, Vol. 15, No. 3. (1998), pp. 277-283. by Paul O. Lewis posted to algorithms inference likelihood methods phylogeny reconstruction by rvosa on 2008-02-07 00:05:34 as
	Type ISTS markers are more informative than cytochrome b in phylogenetic reconstruction of the Mustelidae (Mammalia : Carnivora) [My Copy] Systematic Biology, Vol. 52, No. 5. (2003), pp. 571-593. by K. P. Koepfli, R. K. Wayne posted to animals bayesian carnivora data-mining genetics likelihood mitochondrial nuclear parsimony phylogeny phyloinformatics vertebrates by rvosa on 2008-02-07 00:05:34 as
	Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes [My Copy] Systematic Biology, Vol. 52, No. 4. (2003), pp. 439-459. by C. M. R. Kelly, N. P. Barker, M. H. Villet posted to bayesian classification likelihood markov-chains methods monte-carlo mrp parsimony supertree 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
	Experimental and phylogenetic evidence for floral mimicry in a guild of fly-pollinated plants [My Copy] Biological Journal of the Linnean Society, Vol. 80, No. 2. (2003), pp. 289-304. by S. D. Johnson, R. Alexandersson, H. P. Linder posted to adaptation evolution likelihood phylogeny plants by rvosa on 2008-02-07 00:05:33 as
	A likelihood ratio test to detect conflicting phylogenetic signal [My Copy] Systematic Biology, Vol. 45, No. 1. (1996), pp. 92-98. by J. P. Huelsenbeck, J. J. Bull posted to likelihood methods ratio-test by rvosa on 2008-02-07 00:05:31 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
	True and false gharials: A nuclear gene phylogeny of Crocodylia [My Copy] Systematic Biology, Vol. 52, No. 3. (2003), pp. 386-402. by J. Harshman, C. J. Huddleston, J. P. Bollback, T. J. Parsons, M. J. Braun posted to bayesian genetics likelihood morphology nuclear phylogeny polymerase-chain-reaction ratio-test by rvosa on 2008-02-07 00:05:30 as
	Likelihood-Based Tests of Topologies in Phylogenetics [My Copy] Systematic Biology, Vol. 49, No. 4. (2000), pp. 652-670. by Nick Goldman, Jon P. Anderson, Allen G. Rodrigo posted to likelihood phylogeny ratio-test topology by rvosa on 2008-02-07 00:05:18 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
	Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach [My Copy] Journal of Molecular Evolution, Vol. 17 (1981), pp. 368-376. by Joseph Felsenstein posted to dna estimation evolution likelihood parsimony phylogeny sequence by rvosa on 2008-02-07 00:05:17 as
	Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics [My Copy] Systematic Biology, Vol. 52, No. 5. (2003), pp. 665-673. by P. Erixon, B. Svennblad, T. Britton, B. Oxelman posted to bayesian likelihood markov-chains methods monte-carlo simulation substitution-models by rvosa on 2008-02-07 00:05:17 as
	Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: The phylogeny of Rodentia (Mammalia) [My Copy] Systematic Biology, Vol. 52, No. 5. (2003), pp. 604-617. by R. W. Debry posted to animals bayesian dna likelihood mammals markov-chains monte-carlo nuclear phylogeny phyloinformatics protein rodents vertebrates by rvosa on 2008-02-07 00:05:14 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 likelihood [93 articles] Export

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