BioNica's method [85 articles] Export

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	Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea [My Copy] Journal of Molecular Evolution, Vol. 29, No. 2. (1 August 1989), pp. 170-179. by H. Kishino, M. Hasegawa posted to model method maximum_likelihood by BioNica on 2009-11-12 18:48:09 as
	Information theory and an extension of the maximum likelihood principle [My Copy] In Proceedings of 2nd International Symposium on Information Theory (1973), pp. 267-281. by H. Aikake edited by B. N. Petrov, F. Csaki posted to model method maximum_likelihood classics by BioNica on 2009-11-06 19:11:43 as
	Estimating the Dimension of a Model [My Copy] The Annals of Statistics, Vol. 6, No. 2. (March 1978), pp. 461-464. by G. Schwarz posted to model method maximum_likelihood bayes by BioNica on 2009-11-06 19:01:42 as along with 2 people and 1 group ltitodem sobolevnrm baker-group
	Further analysts of the data by akaike' s information criterion and the finite corrections [My Copy] Communications in Statistics - Theory and Methods, Vol. 7, No. 1. (1978), pp. 13-26. by N. Sugiura posted to model method maximum_likelihood classics by BioNica on 2009-11-06 18:56:10 as along with 1 person fabiobayer
	Phylogeny.fr: robust phylogenetic analysis for the non-specialist [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W465-469. by A. Dereeper, V. Guignon, G. Blanc, et al.S. Audic, S. Buffet, F. Chevenet, J. F. Dufayard, S. Guindon, V. Lefort, M. Lescot, J. M. Claverie, O. Gascuel posted to phyml phylogeny phylogenetic method bioinformatics analyses by BioNica on 2009-10-05 02:33:10 as along with 7 people biovils Eduvernois nlapalu treangen operon druvus sanchezbuelna
	BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data [My Copy] Mol Biol Evol, Vol. 14, No. 7. (1 July 1997), pp. 685-695. by O. Gascuel posted to phylogeny method by BioNica on 2009-09-30 22:59:01 as along with 6 people vingron lizbiogen timflutre swp09 Haggan matsen
	jModelTest: Phylogenetic Model Averaging [My Copy] Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1253-1256. by D. Posada posted to model method dna by BioNica on 2009-09-30 22:19:50 as along with 4 people Garamonfok operon druvus aprasad
	Phylogenetic model evaluation. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 331-364. by Lars Sommer S. Jermiin, Vivek Jayaswal, Faisal Ababneh, John Robinson posted to phylogenetic model method by BioNica on 2009-09-30 19:32:03 as
	MRBAYES: Bayesian inference of phylogenetic trees [My Copy] Bioinformatics, Vol. 17, No. 8. (1 August 2001), pp. 754-755. by John P. Huelsenbeck, Fredrik Ronquist posted to phylogeny phylogenetics phylogenetic method by BioNica on 2009-09-28 19:34:21 as along with 9 people and 1 group ckenaley lmichan druvus treangen bpb rvosa spavey AaronDarling CharlesM FAB-lab
	Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology [My Copy] Systematic Zoology, Vol. 20, No. 4. (1971), pp. 406-416. by W. M. Fitch posted to phylogeny method classics by BioNica on 2009-09-27 20:33:25 as along with 1 person nklee
	A statistical method for evaluating systematic relationships [My Copy] University of Kansas Scientific Bulletin, Vol. 28 (1958), pp. 1409-1438. by R. R. Sokal, C. D. Michener posted to upgma phylogeny method by BioNica on 2009-09-27 19:21:19 as
	ProtTest: selection of best-fit models of protein evolution [My Copy] Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 2104-2105. by F. Abascal, R. Zardoya, D. Posada posted to protein programs model method bioinformatics by BioNica on 2009-09-22 19:13:41 as along with 5 people and 1 group druvus lizbiogen cmzmasek akifumi penka Nie
	Pfam: A comprehensive database of protein domain families based on seed alignments [My Copy] Proteins: Structure, Function, and Genetics, Vol. 28, No. 3. (1997), pp. 405-420. by E. L. L. Sonnhammer, S. R. Eddy, R. Durbin posted to method hmm database bioinformatics by BioNica on 2009-09-19 19:41:20 as
	Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models [My Copy] Mol Biol Evol, Vol. 26, No. 2. (1 February 2009), pp. 255-271. by M. Anisimova, C. Kosiol posted to model method codon by BioNica on 2009-08-26 23:03:31 as along with 3 people chica djkt gjuggler
	Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1663-1676. by N. Rodrigue, C. L. Kleinman, H. Philippe, N. Lartillot posted to model method codon by BioNica on 2009-08-26 22:12:02 as along with 1 person operon
	Models of coding sequence evolution. [My Copy] Briefings in bioinformatics, Vol. 10, No. 1. (1 January 2009), pp. 97-109. by W. Delport, K. Scheffler, C. Seoighe posted to model method codon by BioNica on 2009-08-26 22:08:55 as along with 10 people operon katholt chica dakelley nuin medic0747 michaelbarton treangen druvus nklee
	A comparison of scoring functions for protein sequence profile alignment [My Copy] Bioinformatics, Vol. 20, No. 8. (22 May 2004), pp. 1301-1308. by R. C. Edgar, K. Sjolander posted to alignment method by BioNica on 2009-07-19 20:32:26 as along with 1 person danatcaret
	The HMMER User's Guide [My Copy] (October 2003) by S. Eddy posted to hmm method by BioNica on 2009-07-19 16:35:17 as
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted to blast method by BioNica on 2009-07-05 05:40:33 as along with 68 people and 5 groups rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes idoerg pjcite swp09 kgutwin mcbla cpwardell johanviklund daforerog nlapalu sebk tjimenez shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM References for 3DSim paper EisenLab biomedical-nlp Microbial-Ecology Plantandetc
	Adaptive Evolution Server @ Datamonkey.org, http://www.datamonkey.org/ [My Copy] posted to adaptive evolution method phylogenetic by BioNica on 2009-06-01 14:45:34 as
	Divide-and-Conquer Multiple Sequence Alignment [My Copy] No. 97-02. (1997) by J. Stoye posted to alignment dca method by BioNica on 2009-05-27 21:57:10 as
	HyPhy: hypothesis testing using phylogenies [My Copy] Bioinformatics, Vol. 21, No. 5. (01 March 2005), pp. 676-679. by S. L. K. Pond, S. D. W. Frost, S. V. Muse posted to method phylogeny by BioNica on 2009-05-25 05:12:00 as along with 5 people druvus operon radek Natasha Garamonfok
	PHYLIP (Phylogeny Inference Package) version 3.6 [My Copy] (2005) by J. Felsenstein posted to method phylogeny by BioNica on 2009-05-25 05:04:32 as
	A benchmark of multiple sequence alignment programs upon structural RNAs [My Copy] Nucleic Acids Research, Vol. 33, No. 8. (2005), pp. 2433-2439. by P. P. Gardner, A. Wilm, S. Washietl posted to alignment evaluation method by BioNica on 2009-05-24 21:57:41 as along with 2 people arcticrasta ilh
	Analysis and comparison of benchmarks for multiple sequence alignment. [My Copy] In silico biology, Vol. 6, No. 4. (2006), pp. 321-339. by G. Blackshields, I. M. Wallace, M. Larkin, D. G. Higgins posted to alignment evaluation method by BioNica on 2009-05-24 21:41:46 as
	Evaluation measures of multiple sequence alignments. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 7, No. 1-2. (r 2000), pp. 261-276. by G. H. Gonnet, C. Korostensky, S. Benner posted to alignment method by BioNica on 2009-05-24 21:32:57 as
	A weighting system and algorithm for aligning many phylogenetically related sequences. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 11, No. 5. (October 1995), pp. 543-551. by O. Gotoh posted to alignment method by BioNica on 2009-05-24 21:26:47 as
	MUSCLE: a multiple sequence alignment method with reduced time and space complexity [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004), 113. by Robert Edgar posted to alignment method by BioNica on 2009-05-19 15:13:59 as along with 30 people and 5 groups tomatoe45 rneches gwallau OscarLopez ivanffcc Helenita Joaquin kmma13 khlevy Pal tomjad mgomes hryk natstreet Md_2007 sebk wallacei knaseanka chrn jwm balajis gbart caporaso sriram_s cdallett sanchezbuelna timflutre gisle urgi Ema LabDros References for 3DSim paper Radiation_Damage Stressosome biomedical-nlp
	Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. [My Copy] Nucleic acids research, Vol. 37, No. 3. (22 February 2009), pp. 858-865. by T. Lassmann, O. Frings, E. L. L. Sonnhammer posted to alignment method by BioNica on 2009-05-19 14:42:42 as along with 4 people maria_hauser robfsouza guhjy nuin
	DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 66. by A. R. Subramanian, J. Weyer-Menkhoff, M. Kaufmann, B. Morgenstern posted to alignment method by BioNica on 2009-05-19 14:38:22 as along with 3 people walshtp treangen moborg
	DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment [My Copy] Algorithms for molecular biology : AMB, Vol. 3, No. 1. (27 May 2008), 6. by A. R. Subramanian, M. Kaufmann, B. Morgenstern posted to alignment method by BioNica on 2009-05-19 14:32:52 as along with 7 people Copper_Calcio walshtp druvus treangen operon reyez dquest
	DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment [My Copy] Bioinformatics, Vol. 15, No. 3. (1 March 1999), pp. 211-218. by B. Morgenstern posted to alignment method by BioNica on 2009-05-19 14:29:19 as along with 1 person chad_davis
	Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. [My Copy] Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006) by Timo Lassmann, Erik L. Sonnhammer posted to alignment evaluation method by BioNica on 2009-05-19 14:19:13 as along with 2 people orzenil Haggan
	Weights for data related by a tree. [My Copy] J Mol Biol, Vol. 207, No. 4. (20 June 1989), pp. 647-653. by S. F. Altschul, R. J. Carroll, D. J. Lipman posted to alignment method by BioNica on 2009-05-12 23:55:55 as along with 3 people and 1 group souravc nuke2005 newton1234 iSEEM
	The Multiple Sequence Alignment Problem in Biology [My Copy] SIAM Journal on Applied Mathematics, Vol. 48, No. 5. (1988), pp. 1073-1082. by H. Carrillo, D. Lipman posted to alignment method msa by BioNica on 2009-05-12 23:39:34 as
	Multiple DNA and protein sequence alignment based on segment-to-segment comparison [My Copy] Proceedings of the National Academy of Sciences, Vol. 93, No. 22. (29 October 1996), pp. 12098-12103. by B. Morgenstern, A. Dress, T. Werner posted to alignment method by BioNica on 2009-05-11 19:47:28 as along with 3 people adijr gjuggler newton1234
	Multiple sequence alignment with the divide-and-conquer method [My Copy] Gene, Vol. 211, No. 2. (12 May 1998), pp. GC45-GC56. by J. Stoye posted to alignment dca method by BioNica on 2009-05-11 19:36:46 as
	A general method for fast multiple sequence alignment. [My Copy] Gene, Vol. 172, No. 1. (12 June 1996) by U. Tönges, S. W. Perrey, J. Stoye, A. W. Dress posted to alignment dca method by BioNica on 2009-05-11 19:21:30 as
	DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 13, No. 6. (December 1997), pp. 625-626. by J. Stoye, V. Moulton, A. W. Dress posted to alignment dca method by BioNica on 2009-05-11 19:19:01 as
	DIALIGN: finding local similarities by multiple sequence alignment [My Copy] Bioinformatics, Vol. 14, No. 3. (1 April 1998), pp. 290-294. by B. Morgenstern, K. Frech, A. Dress, T. Werner posted to alignment method by BioNica on 2009-05-11 19:00:42 as along with 2 people and 1 group indigoviolet adijr EisenLab
	Segment-based multiple sequence alignment [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192. by T. Rausch, A. K. Emde, D. Weese, A. Doring, C. Notredame, K. Reinert posted to alignment method by BioNica on 2009-05-07 15:05:57 as along with 9 people nuin darian Md_2007 zwang Ema APRegier djkt aprasad groepl
	Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment [My Copy] Bioinformatics (4 December 2008), btn630. by B. Paten, J. Herrero, K. Beal, E. Birney posted to alignment method by BioNica on 2009-05-04 19:11:01 as along with 9 people guhjy dakelley semrich gjuggler djkt rschulz birney operon druvus
	A general method applicable to the search for similarities in the amino acid sequence of two proteins. [My Copy] Journal of molecular biology, Vol. 48, No. 3. (March 1970), pp. 443-453. by S. B. Needleman, C. D. Wunsch posted to alignment classics method by BioNica on 2009-04-22 18:38:55 as along with 16 people windman83 esyoun stsaft timflutre mcbla db344 DarkMars cawelsh9 sebk jwm dgront rabio incovoma yylin newton1234 Ema
	Evolutionary rate at the molecular level. [My Copy] Nature, Vol. 217, No. 5129. (17 February 1968), pp. 624-626. by M. Kimura posted to classics evolution evolutionary method model phylogeny by BioNica on 2009-04-22 18:08:25 as along with 5 people vprieto renewang gjuggler timflutre elfar
	Construction of phylogenetic trees. [My Copy] Science, Vol. 155, No. 760. (20 January 1967), pp. 279-284. by W. M. Fitch, E. Margoliash posted to classics method phylogeny by BioNica on 2009-04-22 18:07:23 as along with 2 people timflutre treangen
	Progressive sequence alignment as a prerequisite to correct phylogenetic trees. [My Copy] J Mol Evol, Vol. 25, No. 4. (1987), pp. 351-360. by D. F. Feng, R. F. Doolittle posted to alignment method by BioNica on 2009-04-22 17:48:25 as along with 5 people esyoun balajis nuke2005 AaronDarling newton1234
	Kalign--an accurate and fast multiple sequence alignment algorithm. [My Copy] BMC bioinformatics, Vol. 6 (2005) by T. Lassmann, E. L. Sonnhammer posted to alignment method by BioNica on 2009-04-22 17:44:43 as along with 7 people maria_hauser Thaverkamp johanviklund aalibes CharlesM knaseanka Haggan
	Multiple sequence alignments [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 3. (June 2005), pp. 261-266. by I. M. Wallace, G. Blackshields, D. G. Higgins posted to alignment method by BioNica on 2009-04-15 22:31:07 as along with 5 people Thaverkamp martainn mdimmic bpb nklee
	Recent Evolutions of Multiple Sequence Alignment Algorithms [My Copy] PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123. by C. Notredame posted to alignment method by BioNica on 2009-04-15 22:25:48 as along with 9 people and 1 group treangen natstreet druvus giovenko agustinarce skhadar sobolevnrm hpaces mingzhi baker-group
	CTree: comparison of clusters between phylogenetic trees made easy [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2952-2953. by John Archer, David L. Robertson posted to method phylogeny by BioNica on 2009-04-08 02:12:57 as along with 1 person ryanraaum

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method	85
alignment	67
evolution	64
pathogenesis-related	63
chitinases	61
model	36
plant	34
selection	34
phylogeny	30
pr04	30
pr12	30
database	25
pr03	25
defensin	23
protein	23
defense	22
antifungal	20
peroxidase	19
pr08	19
pr11	17
pr13	17
pr02	16
pr14	16
chitin-binding	15
duplication	15
pr09	15
pr17	15
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germin-like	14
glycoside_hydrolases	14
resistance	13
germin	12
paml	12
phylogenetic	12
programs	12
codon	11
homology	11
oxalate-oxidase	11
structure	11
hordeum	10
polyploidy	10
thionin	10
antimicrobial	9
hmm	9
pr10	9
triticum	9
pr05	8
pr06	8
proteins	8
classics	7
hevein	7
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pr01	7
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pr16	7
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allergens	5
darwinian	5
dna	5
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gene_code	5
glucanases	5
positive	5
powdery_mildew	5
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adaptive	4
analyses	4
color	4
dca	4
pr	4
pr07	4
pr5	4
sar	4
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solanum	4
zea	4
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molecular_evolution	3
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njplot	2
peptide	2
phyml	2
r-genes	2
ros	2
signal_transduction	2
tree-puzzle	2
aphid	1
arabidopsis	1
at2g14610	1
at2g37130	1
bacteria	1
basic	1
capsicum	1
cdna	1
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dnatagger	1
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ecosystem	1
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gene-fusion	1
genetic-mapping	1
hybrid	1
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isr	1
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metaphors	1
msa	1
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non-neutral	1
pathogenicity	1
pepper	1
physcomitrella	1
physiology	1
plant-insect	1
pollen	1
powdery-mildew	1
pr18	1
prank	1
proteinase	1
proteinase-inhibitor	1
protein-coding	1
reconstruction	1
review	1
secretory	1
serine_protease	1
superoxide_dismutase	1
synonymous	1
systemic	1
tree-thinking	1
upgma	1
xylanase	1

BioNica's method [85 articles] Export

BioNica's tags