StarBEAST2 statistics

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Citations per year

Number of citations per year for the bioinformatics software tool StarBEAST2
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Tool usage distribution map

This map represents all the scientific publications referring to StarBEAST2 per scientific context
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Protocols

StarBEAST2 specifications

Information


Unique identifier OMICS_17202
Name StarBEAST2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 0.14.0
Stability Stable
Maintained Yes

Subtool


  • FBD-MSC (Fossilized Birth-Death and MultiSpec

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Versioning


No version available

Documentation


Maintainer


  • person_outline Huw Ogilvie

Publications for StarBEAST2

StarBEAST2 citations

 (6)
library_books

Phylogenomics of a rapid radiation: the Australian rainbow skinks

2018
BMC Evol Biol
PMCID: 5800007
PMID: 29402211
DOI: 10.1186/s12862-018-1130-4

[…] icularly near its base. For instance, concatenation and summary coalescent (ASTRAL) analyses inferred strongly that C. jarnoldae is the sister to all other members of this clade (Figs and ), whereas StarBEAST2 analyses of this focal clade (Fig. ) often placed C. gracilis sister to the rest of the clade, or supported a clade consisting of C. jarnoldae and C. gracilis, albeit with low posterior pro […]

library_books

Origins and biogeography of the Anolis crassulus subgroup (Squamata: Dactyloidae) in the highlands of Nuclear Central America

2017
BMC Evol Biol
PMCID: 5740896
PMID: 29268694
DOI: 10.1186/s12862-017-1115-8

[…] incongruences between mitochondrial-only and nuclear-only datasets due to incomplete lineage sorting, we inferred the species tree of our dataset under a Bayesian multispecies coalescent framework in StarBEAST2 [], implemented in BEAST 2.4.7 []. Use of the multispecies coalescent framework have been shown to produce accurate estimates of species trees from independent gene trees, even when gene tr […]

call_split

Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia

2017
Ecol Evol
PMCID: 5756848
PMID: 29321854
DOI: 10.1002/ece3.3640
call_split See protocol

[…] Bayesian MCMC was run for 108generations, with one tree sampled every 1,000 generations.To obtain more accurate divergence times for Macaronesian lineages, we used the coalescent species tree method StarBEAST2 in BEAST v2.4.6 (Drummond et al., ). These analyses were conducted for (1) Azorina, C. jacobaea and C. bravensis, (2) Musschia, and (3) W. lobelioides subsp. lobelioides. We used two combin […]

library_books

Evolutionarily significant units of the critically endangered leaf frog Pithecopus ayeaye (Anura, Phyllomedusidae) are not effectively preserved by the Brazilian protected areas network

2017
Ecol Evol
PMCID: 5689491
PMID: 29177033
DOI: 10.1002/ece3.3261

[…] alculated in pofad (Joly & Bruneau, ) using the genpofad algorithm (Joly, Bryant, & Lockhart, ).To estimate the relationship among discovered BUs, we constructed a lineage tree (=species tree) in the starbeast2 (Bouckaert et al., ; Ogilvie, Bouckaert & Drummond, ) using a Yule prior with a constant population model. To estimate divergence times, we used an uncorrelated log‐linear clock model for R […]

call_split

Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae)

2017
PLoS One
PMCID: 5584756
PMID: 28873089
DOI: 10.1371/journal.pone.0182618
call_split See protocol

[…] s tree reconstructed from consensus sequences obtained for each morphospecies, and the other based on the species tree (excluding the outgroup) obtained in the frame of divergence time estimates with StarBEAST2 [] (see next section). To underline putative cryptic diversity, species delimitation tests were then performed on the species validated by BPP that included more than ten individuals. The t […]

library_books

Validation and description of two new north western Australian Rainbow skinks with multispecies coalescent methods and morphology

2017
PeerJ
PMCID: 5580384
PMID: 28875076
DOI: 10.7717/peerj.3724

[…] species. We apply BPP () and two approaches using Bayes Factors to test species hypotheses: a SNP based approach, BFD* () using SNAPP () and a sequence-based approach, BFD with the recently developed StarBEAST2 method (). We consider three potential species hypotheses: (i) only the two currently defined species are separated; (ii) a three-species hypothesis—two species corresponding to the two mor […]


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StarBEAST2 institution(s)
Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand; Computational Evolution Group, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; School of Biological Sciences, University of Auckland, Auckland, New Zealand; Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA; Department of Computer Science, University of Auckland, Auckland, New Zealand
StarBEAST2 funding source(s)
Supported by a Royal Society of New Zealand Marsden award (16-UOA-277); by an Australian Laureate Fellowship awarded by the Australian Research Council (FL110100104); by the European Research Council under the Seventh Framework Programme of the European Commission (PhyPD: grant agreement number 335529).

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