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DensiTree specifications

Information


Unique identifier OMICS_11542
Name DensiTree
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Tree set files can be imported in NEXUS format as produced by BEAST and MrBayes.
Output data Images can be exported in bitmap formats (PNG, JPG, BMP) and vector format (SVG).
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 2.2.1
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Remco R. Bouckaert

Publications for DensiTree

DensiTree citations

 (64)
library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] logy measured by the normalized Robinson-Foulds distance calculated by the ETE Toolkit 3.1.1 []; the minimum similarity within the cluster was 0.80. The largest clusters of trees were visualized with DensiTree 2.2.5 [] and a strict consensus tree was calculated for each cluster with the consensus_tree.py script in QIIME, using only nodes occurring more than 50% of the time [].Phylogenies of RNA po […]

call_split

Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data

2018
R Soc Open Sci
PMCID: 5936904
PMID: 29765639
DOI: 10.1098/rsos.171615
call_split See protocol

[…] l quality of the analyses inferred by the trends and variance of the estimates of Bayesian posteriors and estimated sample size (ESS), and estimating the number of chains to remove as burn-in.We used DensiTree (v. 2.01; []) to visualize and qualitatively analyse phylogeographic relationships and uncertainty using multiple trees. DensiTree displays the frequency of topologies as the colour of the t […]

library_books

A new fast method for inferring multiple consensus trees using k medoids

2018
BMC Evol Biol
PMCID: 5887197
PMID: 29621975
DOI: 10.1186/s12862-018-1163-8

[…] ts causing the emergence of paralogous alleles.There are several computational tools for analyzing and visualizing sets of incompatible phylogenetic trees, including SplitsTree [], Dendroscope [] and DensiTree []. These programs allow for inferring different kinds of phylogenetic networks which can be viewed as alternatives to multiple consensus trees. Holland et al. [] were among the first to dis […]

library_books

The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex specific ORFs across order Unionoida

2018
BMC Genomics
PMCID: 5870820
PMID: 29587633
DOI: 10.1186/s12864-018-4583-3

[…] tion process [] and 100 million Markov chain Monte Carlo (MCMC) steps [] with samples taken every 1000 steps. A burn in of 10% was performed on the resulting trees. Tree samples were visualized using DensiTree [] included with BEAST version 2.4.6 package [], and compiled into one “best” topology using TreeAnnotator version 1.4 [] and viewed using FigTree version 1.4.3 []. TM domain predictions for […]

library_books

A Bayesian phylogenetic study of the Dravidian language family

2018
R Soc Open Sci
PMCID: 5882685
PMID: 29657761
DOI: 10.1098/rsos.171504

[…] as sisters in both trees. The position of Tulu in the best-supported tree matches Krishnamurti [, p. 21] as it is the first language to split off from the South I group, but it is uncertain (see the DensiTree in the electronic supplementary material, figure S4, see also [,]). The hierarchical grouping of Badga, Toda, Kota and Betta Kurumba is present in both trees; one difference is that the clos […]

call_split

Oat evolution revealed in the maternal lineages of 25 Avena species

2018
Sci Rep
PMCID: 5844911
PMID: 29523798
DOI: 10.1038/s41598-018-22478-4
call_split See protocol

[…] ve assessments of genome relatedness and topological uncertainty. To visualize the topological uncertainties in inferences of oat genome relationship, Bayesian density trees were also generated using DensiTree 2.2.6 software from the MCC trees that were generated using BEAST software with the same settings as described in ESM.Third, a Bayesian inference of divergence times among 25 Avena species w […]

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DensiTree institution(s)
Department of Computer Science, Auckland University, Auckland, New Zealand

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