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node dating specifications

Information


Unique identifier OMICS_15168
Name node dating
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for node dating

library_books

node.dating: dating ancestors in phylogenetic trees in R.

2016 Bioinformatics
PMCID: 5860581
PMID: 28365756
DOI: 10.1093/bioinformatics/btw744

node dating citations

 (37)
call_split

Origin and dispersal of Hepatitis E virus

2018
PMCID: 5837148
PMID: 29410449
DOI: 10.1038/s41426-017-0009-6
call_split See protocol

[…] s of ancestral nodes were estimated using LSD. Branch lengths were also obtained using aBS-REL to account for the effect of variation in selective pressure along branches and to re-estimate ancestral node dating. The cutthroat trout virus sequence was used to root the phylogeny. […]

library_books

The global origins of resistance associated variants in the non structural proteins 5A and 5B of the hepatitis C virus

2018
Virus Evol
PMCID: 5769712
PMID: 29362671
DOI: 10.1093/ve/vex041

[…] built 1,000 bootstrap phylogenetic trees with RAxML v8.2.10 () and a GTR + Γ model of nucleotide substitution. Each tree was rooted with the rtt function of the R package ape () and time scaled with node.dating ().We simultaneously reconstructed the ancestral sequences and country of origin using BEAST v1.8.3 () Markov chain Monte Carlo with two parallel runs per data set each with 10 million gen […]

call_split

Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages

2018
Sci Rep
PMCID: 5760653
PMID: 29317769
DOI: 10.1038/s41598-017-18432-5
call_split See protocol

[…] Beast v1.8.3 was used to estimate a time-calibrated tree with a node-dating strategy. A BEAST XML file was generated by BEAUTi v1.8.3 using an uncorrelated log-normal-distribution relaxed-clock model and a Yule speciation process as the tree prior. The description […]

library_books

Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)

2017
BMC Evol Biol
PMCID: 5715987
PMID: 29202687
DOI: 10.1186/s12862-017-1090-0

[…] To estimate divergence times within Dasyuromorphia, we carried out dated Bayesian analyses of the molecular dataset using node dating. We used a single Independent Gamma Rates (IGR) clock model, implementing a fossilised birth-death tree branching prior that assumed “diversity” sampling [] and a sample probability of 0.8 […]

call_split

Tip dated phylogeny of whirligig beetles reveals ancient lineage surviving on Madagascar

2017
Sci Rep
PMCID: 5567340
PMID: 28831048
DOI: 10.1038/s41598-017-08403-1
call_split See protocol

[…] ssion on the total evidence dating (TED), , under the fossilized birth- death (FBD) process model and the sensitivity analyses performed, see Supplementary Materials. In all analysis, TED as well as node dating, topology and divergence times were inferred simultaneously, hence our inferred divergence times are not dependent on a topology presumed to be known without error. To set a prior on the b […]

call_split

Skeleton of an unusual, cat sized marsupial relative (Metatheria: Marsupialiformes) from the middle Eocene (Lutetian: 44 43 million years ago) of Turkey

2017
PLoS One
PMCID: 5559079
PMID: 28813431
DOI: 10.1371/journal.pone.0181712
call_split See protocol

[…] ssil stem-therian Vincelestes, and the fossil eutherians Asioryctes and Ukhaatherium).The resultant total evidence matrix (available for download as ) was analysed using Bayesian undated and “tip-and-node dating” analysis in MrBayes 3.2.6 [], following the general approach of Beck et al. [, ]. In brief, an appropriate partitioning scheme and set of models was determined for the sequence data using […]


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node dating institution(s)
Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada; BC Centre for Excellence in HIV/AIDS, Vancouver, Canada; Department of Medicine, University of British Columbia, BC, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada
node dating funding source(s)
This work was supported by the Canadian Institutes of Health Research (CIHR Team Grant: HIV Cure Research—The Canadian HIV Cure Research Enterprise; CanCure (HIG-133050)) and by the Bill and Melinda Gates Foundation Award Number OPP1110049.

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