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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

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

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

node dating in publications

 (23)
PMCID: 5837148
PMID: 29410449
DOI: 10.1038/s41426-017-0009-6

[…] 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., to obtain an overview of the geographic distribution of orthohepevirus a genotypes, we combined data from human […]

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 […]

PMCID: 5760653
PMID: 29317769
DOI: 10.1038/s41598-017-18432-5

[…] with half gaps and without gaps and four datasets without bias screened from 129-gene datasets after sequence bias detection., 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. […]

PMCID: 5715987
PMID: 29202687
DOI: 10.1186/s12862-017-1090-0

[…] and keeuna do not appear to be members of dasyuromorphia, whilst barinya and mutpuracinus are of uncertain relationships within the order. divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. […]

PMCID: 5567340
PMID: 28831048
DOI: 10.1038/s41598-017-08403-1

[…] 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 […]


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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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