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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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- person_outline Bradley Jones
Publication for node dating
node dating citations
(37)Origin and dispersal of Hepatitis E virus
[…] 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. […]
The global origins of resistance associated variants in the non structural proteins 5A and 5B of the hepatitis C virus
[…] 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 […]
Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages
[…] 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 […]
Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)
[…] 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 […]
Tip dated phylogeny of whirligig beetles reveals ancient lineage surviving on Madagascar
[…] 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 […]
Skeleton of an unusual, cat sized marsupial relative (Metatheria: Marsupialiformes) from the middle Eocene (Lutetian: 44 43 million years ago) of Turkey
[…] 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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