rvosa's algorithms [114 articles] Export

Recent papers added to rvosa's library classified by the tag algorithms. You can also see everyone's algorithms.

	PhyloExplorer: a web server to validate, explore and query phylogenetic trees [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (18 May 2009), 108. by Vincent Ranwez, Nicolas Clairon, Frederic Delsuc, et al.Saeed Pourali, Nicolas Auberval, Sorel Diser, Vincent Berry posted to algorithms biodiversity classification data-mining databases graph graphics methods phyloinformatics programming software taxonomy by rvosa on 2009-06-27 09:11:43 as along with 1 person and 1 group djkt FAB-lab
	Evolutionary Data Leaping to Web 3.0: Some Highlights From NESCent's Third Hackathon [My Copy] In ASN/SSB/SSE meeting (2009) by Hilmar Lapp, Arlin Stoltzfus, Todd J. Vision, Rutger A. Vos posted to algorithms data-mining databases dbhack1 evolution nexml ontology programming software xml by rvosa on 2009-06-17 10:20:28 as along with 1 group FAB-lab
	Principles for a names-based cyberinfrastructure to serve all of biology [My Copy] Zootaxa, No. 1950. (2008), pp. 153-163. by David J. Patterson, Sarah Faulwetter, Alexey Shipunov posted to algorithms biodiversity classification data-mining databases phyloinformatics programming software taxonomy by rvosa on 2009-06-09 23:07:39 as along with 1 group FAB-lab
	BEAST: Bayesian evolutionary analysis by sampling trees. [My Copy] BMC evolutionary biology, Vol. 7, No. 1. (08 November 2007), 214. by Alexei J. Drummond, Andrew Rambaut posted to algorithms bayesian markov-chains methods nexml phylogeny phyloinformatics software xml by rvosa on 2009-05-22 07:02:10 as along with 4 people and 1 group lizbiogen operon druvus treangen FAB-lab
	A Linear-Time Majority Tree Algorithm [My Copy] Algorithms in Bioinformatics (2003), pp. 216-227. by Nina Amenta, Frederick Clarke, Katherine St. John posted to algorithms graph methods phylogeny phyloinformatics software topology by rvosa on 2008-12-18 02:35:27 as along with 1 group FAB-lab
	A Randomized Linear-time Majority Tree Algorithm [My Copy] European Conference on Computational Biology (27-30 September 2003) by Nina Amenta, Frederick Clarke, Katherine St. John posted to algorithms data-mining methods phylogeny phyloinformatics software by rvosa on 2008-12-18 02:26:42 as along with 1 group 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
	The 2006 NESCent Phyloinformatics Hackathon: A Field Report [My Copy] Evolutionary Bioinformatics, Vol. 3 (2007), pp. 287-296. by Hilmar Lapp, Sendu Bala, James P. Balhoff, et al.Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, Alisha Holloway, Toshiaki Katayama, Paul O. Lewis, Aaron J. Mackey, Brian I. Osborne, William H. Piel, Sergei, Art F. Y. Poon, Wei-Gang Qiu, Jason E. Stajich, Arlin Stoltzfus, Tobias Thierer, Albert J. Vilella, Rutger A. Vos, Christian M. Zmasek, Derrick J. Zwickl, Todd J. Vision posted to algorithms methods programming by rvosa on 2008-08-08 07:37:01 as
	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
	Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2596-2603. by Jean-Francois Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, Francois Rechenmann, Guy Perriere posted to algorithms alignment databases data-mining genome methods phylogenomics phyloinformatics by rvosa on 2008-08-08 07:21:45 as along with 2 people and 2 groups ana stajich structural_bioinformatics Bioinformatics
	Improving the specificity of high-throughput ortholog prediction. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (28 May 2006) by Debra L. Fulton, Yvonne Y. Li, Matthew R. Laird, Benjamin G. Horsman, Fiona M. Roche, Fiona S. Brinkman posted to algorithms alignment data-mining genome homology methods phylogenomics phyloinformatics by rvosa on 2008-08-08 07:17:36 as along with 4 people and 2 groups operon indigoviolet kaspermunch cerca Bioinformatics EisenLab
	BranchClust: A phylogenetic algorithm for selecting gene families [My Copy] BMC Bioinformatics, Vol. 8 (10 April 2007), 120. by Maria S. Poptsova, Peter J. Gogarten posted to algorithms alignment data-mining genome homology methods phylogenomics phyloinformatics programming by rvosa on 2008-08-08 07:02:46 as along with 4 people and 2 groups GustavoLacerda cgaugain dandaman stajich FAB-lab Mycology
	Understanding the Metropolis-Hastings Algorithm [My Copy] The American Statistician, Vol. 49, No. 4. (1995), pp. 327-335. by Siddhartha Chib, Edward Greenberg posted to algorithms bayesian markov-chains methods monte-carlo statistics by rvosa on 2008-05-13 01:30:09 as along with 15 people and 2 groups fordela ashleygeorge Borelli okouma ldietz pcarbo icosma adriandefroment leonnovelo i-stevenson jrw quianominorleo ansobol markusd nojhan FAB-lab Metaheuristics
	Using Perl for Statistics: Data Processing and Statistical Computing [My Copy] Journal of Statistical Software, Vol. 11, No. 1. (May 2004) by Giovanni Baiocchi posted to algorithms data-mining methods programming software by rvosa on 2008-02-08 03:21:56 as
	A novel method for economical diagnosis of cladograms under Sankoff optimization [My Copy] Cladistics, Vol. 10 (1994), pp. 207-213. by Ward C. Wheeler, Kevin Nixon posted to algorithms methods parsimony phylogeny by rvosa on 2008-02-07 00:05:51 as
	Iterative pass optimization of sequence data [My Copy] Cladistics-the International Journal of the Willi Hennig Society, Vol. 19, No. 3. (2003), pp. 254-260. by W. C. Wheeler posted to algorithms alignment methods phylogeny sequence by rvosa on 2008-02-07 00:05:51 as
	Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure [My Copy] Cladistics, Vol. 6 (1990), pp. 269-275. by Ward C. Wheeler posted to algorithms methods parsimony phylogeny weighting by rvosa on 2008-02-07 00:05:51 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
	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
	Distributions of Tree Comparison Metrics - Some New Results [My Copy] Systematic Biology, Vol. 42, No. 2. (1993), pp. 126-141. by M. A. Steel, D. Penny posted to algorithms evolution methods phylogeny topology by rvosa on 2008-02-07 00:05:48 as
	PAUPRat: PAUP* implementation of the parsimony ratchet. [My Copy] (2001) by D. S. Sikes, Paul O. Lewis posted to algorithms methods parsimony software by rvosa on 2008-02-07 00:05:47 as
	Supertree algorithms for ancestral divergence dates and nested taxa [My Copy] Bioinformatics, Vol. 20, No. 0. (2004), pp. 1-6. by C. Semple, P. Daniel, W. Hordijk, Page, M. A. Steel posted to algorithms divergence methods phylogeny supertree by rvosa on 2008-02-07 00:05:47 as
	The neighbor-joining method: a new method for reconstructing phylogenetic trees [My Copy] Molecular Biology and Evolution, Vol. 4 (1987), pp. 406-425. by N. Saitou, M. Nei posted to algorithms methods phenetics phylogeny by rvosa on 2008-02-07 00:05:45 as
	The use of tree comparison metrics [My Copy] Systematic Zoology, Vol. 34 (1985), pp. 75-82. by D. Penny, M. P. Hendy posted to algorithms methods topology by rvosa on 2008-02-07 00:05:42 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
	The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis [My Copy] Cladistics, Vol. 15 (1999), pp. 407-414. by Kevin Nixon posted to algorithms methods parsimony phylogeny by rvosa on 2008-02-07 00:05:39 as
	Dictionary of Algorithms and Data Structures [My Copy] (August 2005) by T. Nis posted to algorithms programming by rvosa on 2008-02-07 00:05:39 as
	Simulated evolutionary optimization and local search: Introduction and application to tree search [My Copy] Cladistics, Vol. 17, No. 1. (2001), pp. S12-S25. by A. Moilanen posted to algorithms methods phylogeny simulation by rvosa on 2008-02-07 00:05:37 as
	Assessing progress in systematics with continuous jackknife function analysis [My Copy] Systematic Biology, Vol. 52, No. 1. (2003), pp. 55-65. by J. A. Miller posted to algorithms characters methods phylogeny weighting by rvosa on 2008-02-07 00:05:37 as
	Equations of state calculations by fast computing machines [My Copy] J. Chem. Phys., Vol. 21 (1953), pp. 1087-1091. by N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, E. Teller posted to algorithms programming by rvosa on 2008-02-07 00:05:37 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
	Markov Chain Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees [My Copy] Molecular Biology and Evolution, Vol. 16, No. 6. (1999), pp. 750-759. by Bret Larget, Donald L. Simon posted to algorithms bayesian markov-chains methods monte-carlo phylogeny by rvosa on 2008-02-07 00:05:34 as
	Quantitative phyletics and the evolution of anurans [My Copy] Systematic Zoology, Vol. 40 (1969), pp. 446-457. by A. G. Kluge, James S. Farris posted to algorithms characters methods by rvosa on 2008-02-07 00:05:34 as
	Homoplasy Increases Phylogenetic Structure [My Copy] Cladistics, Vol. 15 (1999), pp. 91-93. by Mari Kallersjo, Victor A. Albert, James S. Farris posted to algorithms methods parsimony by rvosa on 2008-02-07 00:05:33 as
	Bonsai: teaching a clown to prune trees [My Copy] No. CMPT TR 91-6. (1991) by L. Hafer posted to algorithms programming topology by rvosa on 2008-02-07 00:05:29 as
	Analyzing large data sets in reasonable times: Solutions for composite optima [My Copy] Cladistics, Vol. 15, No. 4. (1999), pp. 415-428. by P. A. Goloboff posted to algorithms methods parsimony phyloinformatics by rvosa on 2008-02-07 00:05:18 as
	The agreement metric for labeled binary trees [My Copy] Mathematical Bioscience, Vol. 123 (1994), pp. 215-226. by W. Goddard, E. Kubicka, G. Kubicki, F. R. Mcmorris posted to algorithms methods phylogeny topology by rvosa on 2008-02-07 00:05:18 as
	Inferring phylogenies from DNA sequences of unequal base compositions [My Copy] Proceedings of the National Academy of Sciences USA, Vol. 92 (1995), pp. 11317-11321. by Nicolas Galtier, Manolo Gouy posted to algorithms genetics markov-chains methods monte-carlo phylogeny by rvosa on 2008-02-07 00:05:17 as
	Confidence limits on phylogenies: an approach using the bootstrap [My Copy] Evolution, Vol. 39 (1985), pp. 783-791. by Joseph Felsenstein posted to algorithms methods phylogeny by rvosa on 2008-02-07 00:05:17 as
	The retention index and the rescaled consistency index [My Copy] Cladistics, Vol. 5 (1989), pp. 417-419. by James S. Farris posted to algorithms characters methods phylogeny topology by rvosa on 2008-02-07 00:05:17 as
	Graph Theory [My Copy] Vol. 173 (2005) by Reinhard Diestel posted to algorithms graph networks topology by rvosa on 2008-02-07 00:05:16 as
	Toward a characterization of landscapes of combinatorial optimization problems, with special attention to the phylogeny problem [My Copy] Journal of Computational Biology, Vol. 2, No. 3. (1995), pp. 439-450. by M. A. Charleston posted to algorithms methods phylogeny by rvosa on 2008-02-07 00:05:12 as
	A method for deducing branching sequences in phylogeny [My Copy] Evolution, Vol. 19 (1965), pp. 311-326. by J. H. Camin, R. R. Sokal posted to algorithms methods phylogeny topology by rvosa on 2008-02-07 00:05:11 as
	Branch support and tree stability [My Copy] Cladistics, Vol. 10 (1994), pp. 295-304. by K. Bremer posted to algorithms methods topology by rvosa on 2008-02-07 00:05:09 as
	Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees [My Copy] Taxon, Vol. 41 (1992), pp. 3-10. by B. R. Baum posted to algorithms data-mining methods mrp phyloinformatics supertree by rvosa on 2008-02-07 00:05:07 as
	Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom [My Copy] BMC Evolutionary Biology, Vol. 7 (09 August 2007), 134. by Eiko E. Kuramae, Vincent Robert, Carlos Echavarri-Erasun, Teun Boekhout posted to algorithms amino-acid data-mining fungi methods phylogenomics phylogeny phyloinformatics protein by rvosa on 2008-02-01 11:30:06 as along with 2 people and 2 groups echinotrix stajich FAB-lab Mycology
	Recent Evolutions of Multiple Sequence Alignment Algorithms [My Copy] PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123. by Cédric Notredame posted to algorithms alignment methods sequence by rvosa on 2008-02-01 11:26:13 as along with 11 people and 2 groups druvus treangen mdimmic timflutre stajich zwang cabbagezs groepl yoanjacquemin marti smbe2008 Bioinformatics FAB-lab
	Profiling Phylogenetic Informativeness [My Copy] Systematic Biology, Vol. 56, No. 2. (2007), pp. 222-231. by Jeffrey P. Townsend posted to algorithms animals characters data-mining mammals methods mice phylogeny phyloinformatics rodents vertebrates by rvosa on 2008-02-01 11:18:22 as along with 4 people and 2 groups gjuggler aprasad stajich Jporci FAB-lab Mycology

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animals	606
vertebrates	463
mammals	447
phylogeny	432
primates	420
evolution	233
methods	230
source-trees	125
dna	123
genetics	117
algorithms	114
mitochondrial	104
comparative	102
likelihood	91
rates	90
speciation	89
substitution-models	88
invertebrates	85
data-mining	84
divergence	83
morphology	82
behaviour	80
classification	79
biodiversity	77
phyloinformatics	77
diversification	76
software	74
sequence-evolution	73
humans	72
clock-like	68
insects	68
encephalization	62
programming	62
reconstruction	62
ecology	58
sequence	57
taxonomy	57
hominidae	56
fossils	55
genome	54
models	52
selection	52
adaptation	51
parsimony	51
bayesian	50
biogeography	49
nuclear	49
parasitism	49
topology	49
dbhack1	48
databases	47
supertree	45
protein	44
characters	42
sociality	40
phylogenomics	36
plants	36
sexual	36
amino-acid	32
xml	32
inference	31
markov-chains	31
morphometrics	31
anthropology	30
monte-carlo	30
extinction	29
bacteria	28
life-history	28
mrp	28
nexml	27
population-genetics	27
alignment	25
contrasts	25
ratio-test	24
karyotyping	20
population	20
radiation	20
lemuridae	19
simulation	19
ontology	18
rodents	18
conservation	17
strepsirrhines	17
birds	16
statistics	15
specialization	14
hybridization	13
viruses	13
predation	12
rna	12
weighting	12
carnivora	11
colobinae	11
fungi	11
homology	11
networks	11
vision	11
polymorphism	10
restriction	10
cebidae	9
fishes	9
graph	9
phenetics	9
recombination	9
chiroptera	8
platyrrhines	8
polymerase-chain-reaction	8
competition	7
lexicostatistics	7
mice	7
proteomics	7
estimation	6
lizards	6
regions	6
alcids	5
cercopithecidae	5
metabolomics	5
cells	4
cercopithecinae	4
graphics	4
rats	4
catarrhines	3
cheirogaleidae	3
sine	3
variability	3
cetartiodactyla	2
haplorhini	2
cattle	1
dogs	1
fingerprinting	1
hylobates	1
line	1
microarray	1
nucleic	1
philosophy	1
shrews	1
songbirds	1
tarsiidae	1

rvosa's algorithms [114 articles] Export

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