Infers trees in which sampled individuals can be direct ancestors of other sampled individuals. This method allows the detection of sampled ancestors as well as the estimation of the probability that an individual will be removed from the process when it is sampled. sampled-ancestors was applied to infer divergence times and diversification rates when fossils are included along with extant species samples, so that fossilisation events are modelled as a part of the tree branching process.

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sampled-ancestors classification

sampled-ancestors specifications

Software type:
Package
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS
Version:
1.1.7
Requirements:
Beast 2
Interface:
Graphical user interface
Input data:
extant sequences, fossil occurrence dates and fixed sampling probability
Computer skills:
Medium
Stability:
Stable

Publications

  • (Gavryushkina et al., 2014) Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol.
    PMID: 25474353

sampled-ancestors support

Documentation

Credits

Institution(s)

Department of Computer Science, University of Auckland, Auckland, New Zealand; Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand; Department of Biosystems Science and Engineering, ETH Zürich, Switzerland

Funding source(s)

This tool was funded by The University of Auckland Doctoral Scholarship; by a Rutherford Discovery Fellowship from the Royal Society of New Zealand; by the European Research Council under the 7th Framework Programme of the European Commission (PhyPD: Grant Agreement Number 335529); and by Marsden grant #UOA1324 from the Royal Society of New Zealand.

Link to literature

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