Datamonkey protocols

View Datamonkey computational protocol

Datamonkey statistics

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Datamonkey specifications

Information


Unique identifier OMICS_16822
Name Datamonkey
Interface Web user interface
Restrictions to use None
Programming languages Perl, R
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • FUBAR (Fast Unconstrained Bayesian AppRoximat
  • PARRIS

Maintainer


  • person_outline Sergei Kosakovsky Pond <>

Publications for Datamonkey

Datamonkey in pipelines

 (48)
2017
PMCID: 5266723
PMID: 28184216
DOI: 10.3389/fmicb.2017.00048

[…] the results requiring that more than one method detected selection and that p-values or posterior probabilities were below 0.05 or 0.9, respectively. hyphy analysis methods were implemented in the datamonkey.org web portal (pond and frost, ). methods tested included single likelihood ancestor counting method (slac; kosakovsky pond and frost, ), fixed effects likelihood method (fel, ifel; pond […]

2017
PMCID: 5723339
PMID: 29259596
DOI: 10.3389/fmicb.2017.02399

[…] calculated from the constructed phylogenetic trees by the patristic program (fourment and gibbs, )., non-synonymous (dn) and synonymous (ds) substitutions rates at each codon were calculated by the datamonkey server to estimate the positive and negative selection sites in capsid vp1 genes of hunov gii.4 and each gii.4 variant (pond and frost, ; delport et al., ). sites under positive (dn > […]

2017
PMCID: 5737360
PMID: 29048530
DOI: 10.1093/gbe/evx199

[…] sequences of venom components from the reference genome were codon-aligned using mafft (), and sites under selection were analyzed using the rel algorithm implemented in the hyphy package on the datamonkey server (; )., a consensus sequence of amino acids was formed from the codon alignment and used as input for developing a pla2 model in swiss-model (; ). the suitable model was selected […]

2016
PMCID: 4748293
PMID: 26861415
DOI: 10.1038/srep20783

[…] pressures on form id rbcl sequences for each dataset were conducted using maximum likelihood-based slac methodology as implemented in the hyphy package and run using web interface at http://www.datamonkey.org. for analyses of natural selection pressure within each ecoregion dataset, automatic nucleotide substitution model selection was undertaken before the slac analysis. the ratio […]


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Datamonkey in publications

 (543)
PMCID: 5915587
PMID: 29691381
DOI: 10.1038/s41426-018-0079-0

[…] differences in enc were calculated using analysis of variance., dn/ds values of all reported avian influenza viral strains and the selected civ and human influenza virus strains were estimated using datamonkey (http://www.datamonkey.org/). alignments were performed using muscle after removing termination codons., the frequencies of 16 dinucleotides per strain were calculated using dambe […]

PMCID: 5919079
PMID: 29694383
DOI: 10.1371/journal.pone.0193525

[…] a conserved and variable amino acids respectively as described earlier []., the selection pressure in the 2nd hvr of g protein gene of the ba9 lineage of the ba genotype was estimated by using the datamonkey webserver [] (http://www.datamonkey.org/). the dataset consisted of 281 sequences from different geographical regions including 28 ba9 strains sequenced in this study (). the synonymous […]

PMCID: 5921268
PMID: 29699483
DOI: 10.1186/s12862-018-1175-4

[…] in oceania region: australia, french polynesia, and samoa.fig. 2, the selection pressure analysis of the complete coding region of denv3/iii was performed using the hyphy package as implemented in datamonkey server []. a combination of codon-based selection pressure analysis (slac, fel, and ifel) with hierarchical bayesian based analysis (fubar) and branch-site based analysis (meme) revealed […]

PMCID: 5910556
PMID: 29721030
DOI: 10.1186/s12983-018-0266-9

[…] of sites between which recombination is inferred was investigated by using the software dnasp [] and the genetic algorithm for recombination detection (gard) as implemented on the webserver datamonkey []. the software geneconv (http://www.math.wustl.edu/~sawyer) [] was used to identify possible past gene conversion events. significant gene conversion tracks were detected by permutation […]

PMCID: 5923487
PMID: 29652824
DOI: 10.3390/v10040193

[…] these putative recombination events. the occurrence of recombination in bagv genomes was also investigated with a method called genetic algorithms for recombination detection (gard) implemented in datamonkey web server (http://datamonkey.org) [], that estimates breakpoints based on a genetic algorithm. the statistical significance of putative breakpoints was evaluated through kishino-hasegawa […]


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Datamonkey institution(s)
Department of Pathology, Antiviral Research Center, University of California, San Diego, CA, USA; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Medicine, Antiviral Research Center, University of California, San Diego, CA, USA
Datamonkey funding source(s)
This work was supported by Joint Division of Mathematical Sciences/National Institute of General Medical Sciences Mathematical Biology Initiative through Grant NSF-0714991; National Institutes of Health (AI43638, AI47745 and AI57167); the University of California University wide AIDS Research Program (grant number IS02- SD-701); University of California, San Diego Center for AIDS Research/NIAID Developmental Award (AI36214); Royal Society Wolfson Research Merit Award; Canadian Institutes of Health Research (CIHR) Fellowships Award in HIV/AIDS Research (200802HFE).

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