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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Alexei Drummond

Publication for sampled-ancestors

sampled-ancestors citations

 (8)
call_split

Quantifying the fitness cost of HIV 1 drug resistance mutations through phylodynamics

2018
PLoS Pathog
PMCID: 5877888
PMID: 29462208
DOI: 10.1371/journal.ppat.1006895
call_split See protocol

[…] itive or resistant) and the phylogenies for each cluster were reconstructed jointly with the epidemiological parameters. While the tree topology, tree height and length, the branch rate variation and sampled ancestors [] were estimated separately for each of the clusters, the substitution rate and epidemiological parameters were estimated jointly for all clusters. The parameters that were estimate […]

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Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature

2017
PeerJ
PMCID: 5602675
PMID: 28929018
DOI: 10.7717/peerj.3782
call_split See protocol

[…] ng, and not setting to normalize the average rate. Particularly relevant for the taxonomic purposes of this study, the FBDSA tree model allows for testing whether one or more of the included taxa are sampled ancestors of one or more other included taxa, as it discriminates between cladogenetic and anagenetic patterns in macroevolution (; and reference therein). We used two tree models included in […]

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Specimen level phylogenetics in paleontology using the Fossilized Birth Death model with sampled ancestors

2017
PeerJ
PMCID: 5335686
PMID: 28265519
DOI: 10.7717/peerj.3055
call_split See protocol

[…] cters were treated as a single partition, and the ’s () model was conditioned to variable characters only using the implementation included in BEAST vers. 2.4.4. The Fossilized Birth-Death model with Sampled Ancestors implemented by was used as tree prior. In this study, the only notable difference from the method used by was the setting of the rho parameter, that defines the probability of samp […]

library_books

Phylogenetic Tools for Generalized HIV 1 Epidemics: Findings from the PANGEA HIV Methods Comparison

2016
Mol Biol Evol
PMCID: 5854118
PMID: 28053012
DOI: 10.1093/molbev/msw217

[…] Phylodynamic analyses were performed in BEAST v2.0 () using the add-ons “bdsky” (), “SA” () and “bdmm” (). Under the birth–death skyline model with sampled ancestors (“SA” module), individuals could transmit with some probability after sampling which improved estimation of the reporting variables in preliminary analyses (round 1 of the exercise). […]

library_books

Bayesian Total Evidence Dating Reveals the Recent Crown Radiation of Penguins

2016
Syst Biol
PMCID: 5410945
PMID: 28173531
DOI: 10.1093/sysbio/syw060

[…] rtainty in the topological placement of the fossil taxa, whereas many clades uniting extant taxa receive substantially higher posterior probabilities.We calculated Bayes factors for all fossils to be sampled ancestors assuming the prior probability that a fossil is a sampled ancestor is defined by the tree prior model conditioned on the number of sampled extant and fossil species and assigned samp […]

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Bayesian phylogenetic estimation of fossil ages

2016
PMCID: 4920331
PMID: 27325827
DOI: 10.1098/rstb.2015.0129
call_split See protocol

[…] a stratigraphic age range for each fossil (with li being the lower age bound for fossil i, and ui being the upper age bound for fossil i), we sample phylogenetic trees with the fossils being tips or sampled ancestors, and each fossil having a specified age in the phylogenetic tree within its stratigraphic age range. The parameters of the fossilized birth–death model are summarized in η, and the p […]


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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 Zürich, 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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