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Clockstar specifications

Information


Unique identifier OMICS_13192
Name Clockstar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data ClockstaR requires two forms of input: the sequence alignments and an estimate of the tree topology.
Input format FASTA, NEWICK
Output data ClockstaR returns a folder with the results of the analysis. It includes a file with the partition assignments at the optimal value of k, tables with the sBSDmin and tree scaling factors (s) and two files containing a dendrogram of sBSDmin, a plot of the Gap statistic and the partition assignments for values of k from k = 1 to k = N−1
Output format PDF, TXT
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

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  • person_outline Sebastiàn Duchêne <>

Publication for Clockstar

Clockstar in publications

 (4)
PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4

[…] sequence data from recent studies–, , – (supplementary data ), aligned a set of 11 nuclear loci using macse and mafft, and set nucleotide substitution and clock models using partition finder and clockstar. we reconstructed a set of dated backbone trees using a combination of raxml and beast2 and a database of >500 fossil taxa. we used both conventional node calibration (nc), testing […]

PMCID: 5664179
PMID: 28993654
DOI: 10.1038/s41559-017-0331-3

[…] partitions were inferred with partitionfinder using 20% relaxed clustering with the rcluster_f command. the best-fit number of relaxed molecular clock models for use in beast 2 were inferred with clockstar using default parameters. one molecular clock was inferred to be most appropriate for this dataset. a relaxed molecular clock with a lognormal distribution and a yule tree model was used. […]

PMCID: 5790132
PMID: 29029343
DOI: 10.1093/sysbio/syx061

[…] but is also used in divergence time estimation. because the number of possible partition schemes is often too large (), heuristic algorithms are used in the search for the best-fit scheme. clockstar is another automatic approach for “estimating” the best partition scheme for a given data set, especially suited to bayesian divergence time estimation (). this uses the maximum likelihood […]

PMCID: 5312533
PMID: 28209119
DOI: 10.1186/s12864-017-3555-3

[…] to describe substitution rates across multiple loci, thereby improving the accuracy of divergence-time estimation []. optimal scheme for partitioning of the molecular clock(s) was tested for using clockstar 2.0.1 []. the ml phylogenetic tree topology from the 77 concatenated pcgs was used for divergence time estimation, and the ml branch lengths were estimated using the baseml program in paml […]


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Clockstar institution(s)
School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
Clockstar funding source(s)
This work was supported by the Australian Research Council.

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