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BUCKy specifications


Unique identifier OMICS_06056
Name BUCKy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for BUCKy

BUCKy citations


Practical considerations for plant phylogenomics

Appl Plant Sci
PMCID: 5895195
PMID: 29732268
DOI: 10.1002/aps3.1038

[…] n be concatenated into a supermatrix or used for gene‐tree‐based methods of phylogenetic reconstruction, including ASTRAL‐III (Mirarab et al., ; Zhang et al., ), ASTRID (Vachaspati and Warnow, ), and BUCKy (Larget et al., ). This is especially useful with exon capture and Hyb‐Seq approaches, because loci are likely to be long enough to contain many variable sites and produce gene trees with high c […]


Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

PMCID: 5867853
PMID: 29495636
DOI: 10.3390/genes9030132

[…] dataset into quartets of species. These quartet-based methods (e.g., the summary method Accurate Species TRee ALgorithm (ASTRAL) [,,], the site-based method SVDQuartets [], and a hybrid method called Bucky–Quartet []) rely on the fact that, for a quartet of species, where only three unrooted tree topologies are possible, the species tree topology has the highest probability of occurring in unroote […]


Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

PMCID: 5829208
PMID: 29445022
DOI: 10.1098/rspb.2017.2732

[…] starting trees sampling every 500 generations. For RAXML, 1000 rapid bootstrap searches were performed using the Rapid Bootstrapping algorithm. To assess tree concordance across the RAD loci, we used BUCKy []. First, we split the concatenated RAD alignment into 1000 bp alignments (approx. 7 RAD loci per alignment). Subsequently, we built individual Bayesian trees using MrBayes 3.6 (5 million gener […]


The Highly Divergent Mitochondrial Genomes Indicate That the Booklouse, Liposcelis bostrychophila (Psocoptera: Liposcelididae) Is a Cryptic Species

PMCID: 5844292
PMID: 29352078
DOI: 10.1534/g3.117.300410
call_split See protocol

[…] mated combining results from duplicated analysis, with the first 25% generations discarded.Concordance analysis was conducted to test the concatenation of all mt genes for phylogenetic analyses using BUCKy (; ), which took the files generated by MrBayes for all 14 mt genes and output a greedy consensus tree. A concordance factor (CF) was calculated for each clade of two datasets, and revealed the […]


Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae)

BMC Evol Biol
PMCID: 5729518
PMID: 29237395
DOI: 10.1186/s12862-017-1095-8

[…] yses with MrBayes using the same settings as for the full concatenated analysis, but reducing the number of generations and sampling frequency to 10 million and 1000, respectively. I used the program BUCKy 1.4.4 [, ] to conduct a Bayesian concordance analysis, using the individual gene trees as input. […]


Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum

PMCID: 5717386
PMID: 29208741
DOI: 10.1128/mBio.01339-17

[…] To shed light on the extent of genealogical concordance at a finer scale in the genome, we performed a Bayesian concordance analysis (BCA) using BUCKy v.1.4.4 (, ). BUCKy estimates the level of concordance among multiple genealogies and uses it to infer the tree with the most concordant nodes, which is considered an estimate of the species tre […]


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BUCKy institution(s)
Department of Statistics, University of Wisconsin-Madison, WI, USA

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