Datamonkey pipeline

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

 (27)
2018
PMCID: 5799169
PMID: 29403002
DOI: 10.1038/s41598-018-19312-2

[…] individual values of dn and ds were also obtained. tests for positive selection on individual codons were conducted using the fast unconstrained bayesian approximation (fubar) method as in the datamonkey server41. in all cases, dn − ds estimates were based on input neighbor joining trees inferred using the mg94 nucleotide substitution model. in order to avoid false-positives, only sites […]

2017
PMCID: 5370153
PMID: 28350846
DOI: 10.1371/journal.pone.0174599

[…] strains and trimmed to fragments of 2305 bp., a dna substitution hasegawa-kishono-yano (hky85) model with the best fit for analysis of the c. psittaci ompa and rrn sequences was calculated using datamonkey webserver [31]. dendrograms were constructed using neighbor joining (nj) with the robustness of the clusters assessed by bootstrapping 1000 replicates. mean nucleotide distances among c. […]

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

[…] from the constructed phylogenetic trees by the patristic program (fourment and gibbs, 2006)., 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, 2005; delport et al., 2010). sites under positive […]

2017
PMCID: 5850136
PMID: 28541576
DOI: 10.1093/molbev/msx168

[…] curation. the d. willistoni and obscura group toll-3/4s were less well-aligned and so retained 90% and 63% of alignment positions following gblocks, respectively. we uploaded each alignment to the datamonkey server (pond and frost 2005) and ran the automated substitution model selection program. to test for recombination, we ran each alignment through gard (kosakovsky pond 2006) using […]

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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