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sampled-ancestors specifications

Information


Unique identifier OMICS_14521
Name sampled-ancestors
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Extant sequences, fossil occurrence dates and fixed sampling probability
Operating system Unix/Linux, Mac OS
Computer skills Medium
Version 1.1.7
Stability Stable
Requirements
Beast
Maintained Yes

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Maintainer


  • person_outline Alexei Drummond <>

Publication for sampled-ancestors

sampled-ancestors in publications

 (4)
PMCID: 5877888
PMID: 29462208
DOI: 10.1371/journal.ppat.1006895

[…] estimates are given in table 4 within ., our results suggest that once the patient samples are taken, the patients are unlikely to continue transmitting to others. in fact, the median number of sampled ancestors for most rmds clusters is zero. very few clusters belonging to the 215d, 108i, 181c and 190a data sets have significantly more than zero sampled ancestors. overall, the probability […]

PMCID: 5890724
PMID: 29637019
DOI: 10.7717/peerj.4553

[…] assessment of clocklike behavior (for further description of all methods, as well as all data and scripts used, see )., tip-dating in beast2 (; ) with birth-death-serial sampling (bdss) or sa-bdss (sampled ancestors) tree models (; ) requires a specialized xml input file. to set this up, we used beastmaster (; ; ), a set of r functions that convert nexus character matrices, an excel file […]

PMCID: 5335686
PMID: 28265519
DOI: 10.7717/peerj.3055

[…] at the boundary between micro- and macroevolution (). the recognition of ancestor-descendant relationships in fossils is debated (; ; ; ). in this study, 95% of the sampled trees include a number of sampled ancestors ranging between 0 and 14 (median value, 7; ). this value suggests that up to 23% of the specimens collected in the sample may represent members of populations that are anagenetic […]

PMCID: 5410945
PMID: 28173531
DOI: 10.1093/sysbio/syw060

[…] until recently, combining the fbd model with a total-evidence dating approach was complicated by the fact that existing implementations of the mcmc algorithm over tree space did not allow trees with sampled ancestors. addressed this problem and enabled full bayesian inference using fbd model in the beast2 software () with the sa package (https://github.com/compevol/sampled-ancestors). […]


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sampled-ancestors 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 Z├╝rich, Switzerland
sampled-ancestors 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.

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