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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
	Pathogenesis-related proteins [My Copy] Plant Molecular Biology, Vol. 4, No. 2. (1 March 1985), pp. 111-116. by L. C. Van Loon posted to pr pathogenesis-related by BioNica on 2009-10-31 19:36:34 as along with 1 person biovils
	Analysis of two novel classes of plant antifungal proteins from radish (Raphanus sativus L.) seeds. [My Copy] The Journal of biological chemistry, Vol. 267, No. 22. (5 August 1992), pp. 15301-15309. by F. R. Terras, H. M. Schoofs, M. F. De Bolle, et al.F. Van Leuven, S. B. Rees, J. Vanderleyden, B. P. Cammue, W. F. Broekaert posted to pr12 defensin antifungal by BioNica on 2009-10-31 19:17:21 as along with 1 person biovils
	In Vitro Antifungal Activity of a Radish (Raphanus sativus L.) Seed Protein Homologous to Nonspecific Lipid Transfer Proteins. [My Copy] Plant physiology, Vol. 100, No. 2. (October 1992), pp. 1055-1058. by F. R. Terras, I. J. Goderis, F. Van Leuven, J. Vanderleyden, B. P. Cammue, W. F. Broekaert posted to pr14 antifungal by BioNica on 2009-10-31 18:58:55 as along with 1 person biovils
	Improved prediction of signal peptides: SignalP 3.0. [My Copy] Journal of molecular biology, Vol. 340, No. 4. (16 July 2004), pp. 783-795. by J. D. Bendtsen, H. Nielsen, G. von Heijne, S. Brunak posted to bioinformatics by BioNica on 2009-10-29 22:01:10 as along with 10 people azazello tfuji rpetrenko katholt nedwards kreibich niallhaslam richter80 sebk raiyar
	Duplicated Paralogous Genes Subject to Positive Selection in the Genome of Trypanosoma brucei [My Copy] PLoS ONE, Vol. 3, No. 5. (28 May 2008), e2295. by Richard D. Emes, Ziheng Yang posted to positive paml by BioNica on 2009-10-28 16:23:42 as along with 1 person druvus
	The role of phytohormones ethylene and auxin in plant-nematode interactions [My Copy] Russian Journal of Plant Physiology, Vol. 56, No. 1. (1 January 2009), pp. 1-5. by O. Gutierrez, M. Wubben, M. Howard, B. Roberts, E. Hanlon, J. Wilkinson posted to sar plant-pathogen plant defense by BioNica on 2009-10-25 21:02:10 as
	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
	Model Selection and Multi-model Inference: A Practical Information-Theoretic Approach [My Copy] (2002) by K. P. Burnham, D. R. Anderson posted to model by BioNica on 2009-10-01 20:15:04 as
	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
	Models of Molecular Evolution and Phylogeny [My Copy] Genome Research, Vol. 8, No. 12. (1 December 1998), pp. 1233-1244. by Pietro LiÃ², Nick Goldman posted to molecular model evolution dna by BioNica on 2009-09-30 19:31:12 as along with 5 people seb1 operon gjuggler hdopazo timflutre
	Different versions of the Dayhoff rate matrix. [My Copy] Molecular biology and evolution, Vol. 22, No. 2. (February 2005), pp. 193-199. by C. Kosiol, N. Goldman posted to protein model by BioNica on 2009-09-30 19:10:47 as along with 2 people bpb Haggan
	Amino acid substitution matrices from protein blocks. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919. by S. Henikoff, J. G. Henikoff posted to protein model by BioNica on 2009-09-30 17:43:20 as along with 14 people rshe rpetrenko maria_hauser cmura alefox j3xucite sebk cen4ik kaarsinogen dgront gurkanbebek Iden-J_GluR cjeans ashwinma
	An improved general amino acid replacement matrix. [My Copy] Molecular biology and evolution, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320. by S. Q. Le, O. Gascuel posted to protein model by BioNica on 2009-09-30 17:33:24 as along with 5 people and 1 group lizbiogen druvus stajich friendpine dmp Mycology
	Modeling amino acid replacement. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 7, No. 6. (2000), pp. 761-776. by T. Müller, M. Vingron posted to protein model by BioNica on 2009-09-30 17:31:36 as
	A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. [My Copy] Molecular biology and evolution, Vol. 18, No. 5. (1 May 2001), pp. 691-699. by S. Whelan, N. Goldman posted to protein model by BioNica on 2009-09-30 17:29:48 as along with 7 people calderonv michaelbarton bpb chrn ssgong gjuggler gisle
	The rapid generation of mutation data matrices from protein sequences. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 8, No. 3. (June 1992), pp. 275-282. by D. T. Jones, W. R. Taylor, J. M. Thornton posted to protein model by BioNica on 2009-09-30 17:22:13 as along with 2 people ssgong skumagai
	A model of evolutionary change in proteins [My Copy] In Atlas of Protein Sequence and Structure (1978), pp. 345-352. by M. O. Dayhoff, R. M. Schwartz, B. C. Orcutt edited by M. O. Dayhoff posted to protein model evolution by BioNica on 2009-09-30 17:20:18 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
	HMM Logos for visualization of protein families. [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (21 January 2004), 7. by B. Schuster-Böckler, J. Schultz, S. Rahmann posted to programs hmm by BioNica on 2009-09-22 23:51:36 as along with 2 people analogAI pansapiens
	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
	HAPPY BIRTHDAY: 80 Years of Watching the Evolutionary Scenery [My Copy] Science, Vol. 305, No. 5680. (2 July 2004), pp. 46-47. by Ernst Mayr posted to evolution by BioNica on 2009-09-13 16:14:29 as along with 2 people phoenixzxl Borelli
	Pyoverdine Receptor: a Case of Positive Darwinian Selection in Pseudomonas aeruginosa [My Copy] J. Bacteriol., Vol. 187, No. 10. (15 May 2005), pp. 3289-3292. by Burkhard Tummler, Pierre Cornelis posted to selection darwinian adaptive by BioNica on 2009-09-13 16:08:06 as
	Phylogenetic analysis. Models and estimation procedures. [My Copy] American journal of human genetics, Vol. 19, No. 3 Pt 1. (May 1967), pp. 233-257. by L. L. Cavalli-Sforza, A. W. Edwards posted to phylogenetic model classics by BioNica on 2009-09-07 21:24:33 as along with 1 person druvus
	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
	Dendroscope: An interactive viewer for large phylogenetic trees [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (22 November 2007), 460. by D. Huson, R. Richter, C. Rausch, T. Dezulian, M. Franz, R. Rupp posted to programs phylogeny njplot by BioNica on 2009-08-18 20:45:24 as along with 2 people laughcry gjuggler
	WWW-query: An on-line retrieval system for biological sequence banks [My Copy] Biochimie, Vol. 78, No. 5. (1996), pp. 364-369. by G. Perrière, M. Gouy posted to programs phylogeny njplot by BioNica on 2009-08-18 20:24:27 as
	Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment [My Copy] Genome Biol Evol, Vol. 1, No. 1. (22 June 2009), pp. 114-118. by A. Schneider, A. Souvorov, N. Sabath, G. Landan, G. H. Gonnet, D. Graur posted to selection discussion database darwinian by BioNica on 2009-08-14 17:33:03 as along with 4 people druvus natstreet aprasad gjuggler
	High conservation among sequences encoding type-V thionins in wheat and Aegilops. [My Copy] Plant physiology, Vol. 107, No. 4. (April 1995), pp. 1475-1476. by A. Castagnaro, A. Segura, F. García-Olmedo posted to pr13 thionin triticum by BioNica on 2009-08-07 19:12:40 as
	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
	Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids [My Copy] (April 1998) by R. Durbin, S. R. Eddy, A. Krogh, G. Mitchison posted to hmm by BioNica on 2009-07-19 17:07:12 as
	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
	Statistical Methods in Bioinformatics : An Introduction [My Copy] (20 April 2001) by W. J. Ewens, G. Grant posted to bioinformatics by BioNica on 2009-07-19 14:51:50 as
	A PRp27 gene of Nicotiana benthamiana contributes to resistance to Pseudomonas syringae pv. tabaci but not to Colletotrichum destructivum or Colletotrichum orbiculare [My Copy] Functional Plant Biology, Vol. 36, No. 4. (2009), pp. 351-361. by W. Xie, P. H. Goodwin posted to pathogenesis-related pr17 resistance by BioNica on 2009-07-09 20:24:40 as
	Insights into corn genes derived from large-scale cDNA sequencing. [My Copy] Plant molecular biology, Vol. 69, No. 1-2. (January 2009), pp. 179-194. by N. N. Alexandrov, V. V. Brover, S. Freidin, et al.M. E. Troukhan, T. V. Tatarinova, H. Zhang, T. J. Swaller, Y. P. Lu, J. Bouck, R. B. Flavell, K. A. Feldmann posted to dna pr17 by BioNica on 2009-07-08 19:04:29 as
	Specific patterns of changes in wheat gene expression after treatment with three antifungal compounds. [My Copy] Plant molecular biology, Vol. 57, No. 5. (March 2005), pp. 693-707. by F. Pasquer, E. Isidore, J. Zarn, B. Keller posted to antifungal pr17 by BioNica on 2009-07-07 22:03:00 as
	Isolation and characterisation of a class of carbohydrate oxidases from higher plants, with a role in active defence. [My Copy] The Plant journal : for cell and molecular biology, Vol. 39, No. 2. (July 2004), pp. 147-160. by J. H. Custers, S. J. Harrison, M. B. Sela-Buurlage, et al.E. van Deventer, W. Lageweg, P. W. Howe, P. J. van der Meijs, A. S. Ponstein, B. H. Simons, L. S. Melchers, M. H. Stuiver posted to pathogenesis-related pr18 by BioNica on 2009-07-07 21:15:28 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
	Stomatal Size in Fossil Plants: Evidence for Polyploidy in Majority of Angiosperms [My Copy] Science, Vol. 264, No. 5157. (15 April 1994), pp. 421-424. by J. Masterson posted to polyploidy by BioNica on 2009-06-30 22:26:14 as
	On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. [My Copy] (1859) by C. R. Darwin posted to darwin evolution selection by BioNica on 2009-06-30 17:02:45 as

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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
expression	14
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
phylogenetics	7
pr01	7
pr15	7
pr16	7
bioinformatics	6
evaluation	6
family	6
maximum_likelihood	6
modeling	6
plant-pathogen	6
plant-pathogenic	6
allergens	5
darwinian	5
dna	5
evolutionary	5
gene_code	5
glucanases	5
positive	5
powdery_mildew	5
pr1	5
wound-inducible	5
adaptive	4
analyses	4
color	4
dca	4
pr	4
pr07	4
pr5	4
sar	4
simulations	4
solanum	4
zea	4
antibiotic	3
classification	3
gymnosperms	3
likelihood	3
molecular_evolution	3
mutation	3
oxidative_burst	3
speciation	3
synergy	3
bayes	2
bayesian	2
blast	2
bootstrap	2
darwin	2
discussion	2
disease	2
ferrofluids	2
infection	2
inhibitor	2
molecular	2
multigenic	2
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
cross-linking	1
dnatagger	1
ecology	1
ecosystem	1
fungal	1
gene-fusion	1
genetic-mapping	1
hybrid	1
induced	1
induction	1
isr	1
leaf-gall	1
malus	1
metabolism	1
metaphors	1
msa	1
nbd-arc	1
nectarin	1
neurobiology	1
neutral	1
neutrality	1
nicotiana	1
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

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