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Protocols

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 citations

 (657)
library_books

Polymorphism in merozoite surface protein 7E of Plasmodium vivax in Thailand: Natural selection related to protein secondary structure

2018
PLoS One
PMCID: 5931635
PMID: 29718980
DOI: 10.1371/journal.pone.0196765

[…] phic subregion where significantly greater dN than dS was observed (Tables and ).Codon-based tests for departure from neutrality using SLAC, FEL, iFEL, REL, FUBAR and MEME methods implemented in the Datamonkey Wed-Server have identified 2, 8, 11, 39, 12 and 20 positively selected sites, respectively. Likewise, the TreeSAAP program that determined significant alteration in various physicochemical […]

library_books

BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics

2018
PLoS One
PMCID: 5919079
PMID: 29694383
DOI: 10.1371/journal.pone.0193525

[…] 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 (dS […]

call_split

Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

2018
PMCID: 5915587
PMID: 29691381
DOI: 10.1038/s41426-018-0079-0
call_split See protocol

[…] 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. […]

library_books

Emergence of the Asian lineage dengue virus type 3 genotype III in Malaysia

2018
BMC Evol Biol
PMCID: 5921268
PMID: 29699483
DOI: 10.1186/s12862-018-1175-4

[…] 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 th […]

library_books

Meta populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus)

2018
Front Zool
PMCID: 5910556
PMID: 29721030
DOI: 10.1186/s12983-018-0266-9

[…] rmination 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 t […]

library_books

Detection and characterisation of coronaviruses in migratory and non migratory Australian wild birds

2018
Sci Rep
PMCID: 5899083
PMID: 29654248
DOI: 10.1038/s41598-018-24407-x

[…] irus sequence (Genbank accession: NC_001451.1). Absence of evidence of recombination was confirmed using the Genetic Algorithm Recombination Detection (GARD) method of the HyPhy package hosted on the DataMonkey webserver. Codon specific selection pressure was analysed using the single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL) and […]

Citations

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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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