BioNica's paml [13 articles] Export

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

	User Guide, PAML: Phylogenetic Analysis by Maximum Likelihood [My Copy] (September 2009) by Z. Yang posted to paml method by BioNica on 2009-11-28 20:11:44 as
	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
	PAML 4: phylogenetic analysis by maximum likelihood. [My Copy] Molecular biology and evolution, Vol. 24, No. 8. (1 August 2007), pp. 1586-1591. by Z. Yang posted to phylogenetics paml likelihood bayesian by BioNica on 2007-08-10 21:08:32 as along with 13 people and 1 group ckenaley biomcgary michaelbarton dquest druvus operon akifumi hdopazo stajich ryanraaum RamuAnandakrishnan CharlesM Ema Mycology
	Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. [My Copy] Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 32-43. by Z. Yang, R. Nielsen posted to paml by BioNica on 2006-09-29 14:22:27 as along with 9 people and 1 group katholt bjorns fernan hdopazo timflutre Garamonfok ankur_iitg RamuAnandakrishnan Ema BioinfoCIPF
	The power of phylogenetic comparison in revealing protein function. [My Copy] Proc Natl Acad Sci U S A (22 February 2005) by Z. Yang posted to paml selection by BioNica on 2006-09-29 12:46:12 as along with 6 people and 1 group gjuggler mdimmic stevanspringer bpb tale bpcusack FAB-lab
	Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene [My Copy] Genetics, Vol. 148, No. 3. (1 March 1998), pp. 929-936. by R. Nielsen, Z. Yang posted to paml by BioNica on 2006-09-29 12:33:26 as
	PAML: a program package for phylogenetic analysis by maximum likelihood. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 13, No. 5. (October 1997), pp. 555-556. by Z. Yang posted to paml by BioNica on 2006-09-29 12:32:43 as along with 15 people and 3 groups seb1 thegoose2 alexeid druvus jmjimenez bjorns chrn chad_davis indigoviolet penka stajich pv usagi-kirin tharris skumagai EisenLab Nie Mycology
	Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. [My Copy] Genetics, Vol. 168, No. 2. (1 October 2004), pp. 1041-1051. by W. S. W. Wong, Z. Yang, N. Goldman, R. Nielsen posted to paml selection simulations by BioNica on 2006-09-29 12:30:28 as along with 6 people katholt renewang Natasha timflutre gjuggler CharlesM
	Statistical methods for detecting molecular adaptation [My Copy] Trends in Ecology & Evolution, Vol. 15, No. 12. (1 December 2000), pp. 496-503. by Z. Yang, J. P. Bielawski posted to paml selection by BioNica on 2006-09-29 12:30:11 as
	Detecting amino acid sites under positive selection and purifying selection. [My Copy] Genetics (16 January 2005) by T. Massingham, N. Goldman posted to paml by BioNica on 2006-09-29 12:28:23 as along with 6 people and 1 group MRCBIRD gjuggler gwallau stevanspringer operon Natasha FAB-lab
	Positive selection driving diversification in plant secondary metabolism [My Copy] PNAS, Vol. 103, No. 24. (13 June 2006), pp. 9118-9123. by M. Benderoth, S. Textor, A. J. Windsor, T. Mitchell-Olds, J. Gershenzon, J. Kroymann posted to paml by BioNica on 2006-09-29 12:20:36 as along with 2 people and 1 group haloin cmm FAB-lab
	Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection [My Copy] Molecular Biology and Evolution, Vol. 22, No. 4. (April 2005), pp. 1107-1118. by Z. Yang, W. S. W. Wong, R. Nielsen posted to paml by BioNica on 2006-09-29 12:14:19 as along with 6 people and 1 group rabu Natasha stajich Garamonfok skumagai CharlesM Mycology
	Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites [My Copy] Genetics, Vol. 155, No. 1. (1 May 2000), pp. 431-449. by Z. Yang, R. Nielsen, N. Goldman, A-M K. Pedersen posted to paml by BioNica on 2006-09-29 12:05:40 as along with 8 people druvus fernan Natasha dylan77 Garamonfok tale gjuggler emptyhb

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method	86
alignment	67
evolution	64
pathogenesis-related	63
chitinases	61
model	36
plant	34
selection	34
pr12	30
phylogeny	30
pr04	30
database	25
pr03	25
protein	23
defensin	23
defense	22
antifungal	20
pr08	19
peroxidase	19
pr11	17
pr13	17
pr02	16
pr14	16
pr09	15
duplication	15
pr17	15
chitin-binding	15
expression	14
germin-like	14
glycoside_hydrolases	14
resistance	13
paml	13
phylogenetic	12
germin	12
programs	12
homology	11
oxalate-oxidase	11
codon	11
structure	11
hordeum	10
polyploidy	10
thionin	10
triticum	9
hmm	9
antimicrobial	9
pr10	9
proteins	8
pr05	8
pr06	8
hevein	7
pr15	7
phylogenetics	7
pr16	7
classics	7
pr01	7
family	6
evaluation	6
plant-pathogenic	6
modeling	6
bioinformatics	6
maximum_likelihood	6
plant-pathogen	6
wound-inducible	5
dna	5
powdery_mildew	5
allergens	5
glucanases	5
evolutionary	5
pr1	5
gene_code	5
darwinian	5
positive	5
zea	4
color	4
adaptive	4
analyses	4
solanum	4
pr07	4
pr	4
simulations	4
pr5	4
dca	4
sar	4
likelihood	3
classification	3
oxidative_burst	3
mutation	3
gymnosperms	3
antibiotic	3
speciation	3
synergy	3
molecular_evolution	3
disease	2
peptide	2
molecular	2
bayesian	2
discussion	2
ferrofluids	2
blast	2
tree-puzzle	2
bayes	2
bootstrap	2
infection	2
r-genes	2
signal_transduction	2
ros	2
njplot	2
inhibitor	2
multigenic	2
phyml	2
darwin	2
msa	1
hybrid	1
capsicum	1
plant-insect	1
physiology	1
synonymous	1
nectarin	1
physcomitrella	1
prank	1
protein-coding	1
proteinase	1
dnatagger	1
leaf-gall	1
powdery-mildew	1
metaphors	1
nbd-arc	1
xylanase	1
proteinase-inhibitor	1
nicotiana	1
neutral	1
pr18	1
induction	1
pollen	1
arabidopsis	1
aphid	1
malus	1
gene-fusion	1
systemic	1
upgma	1
neutrality	1
secretory	1
pepper	1
non-neutral	1
neurobiology	1
pathogenicity	1
tree-thinking	1
superoxide_dismutase	1
bacteria	1
induced	1
cross-linking	1
review	1
isr	1
cdna	1
metabolism	1
reconstruction	1
ecosystem	1
ecology	1
genetic-mapping	1
fungal	1
at2g37130	1
basic	1
serine_protease	1
at2g14610	1

BioNica's paml [13 articles] Export

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