DensiTree protocols

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DensiTree statistics

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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

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Documentation


Maintainer


  • person_outline Remco R. Bouckaert <>

Publications for DensiTree

DensiTree in pipeline

2016
PMCID: 4860686
PMID: 26979797
DOI: 10.1093/gbe/evw053

[…] 8 using the gtrcat model and 100 bootstrap replicates., to visualize phylogenetic discordance between loci, we used the best ml tree for each contig from the per-locus raxml analysis to produce densitree plots using densitree version 2.2.1 (). for each gene tree, nodes with bootstrap support <75% were collapsed using the prunetree function in the phangorn package () in r 3.1.2 (r core […]


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DensiTree in publications

 (53)
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] 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 […]

PMCID: 5936904
PMID: 29765639
DOI: 10.1098/rsos.171615

[…] 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 […]

PMCID: 5887197
PMID: 29621975
DOI: 10.1186/s12862-018-1163-8

[…] 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 […]

PMCID: 5882685
PMID: 29657761
DOI: 10.1098/rsos.171504

[…] mutation rates (marginal l = −4131). the mcc tree of the best-fitting model, including posterior support values for the nodes and a scale giving time in years before present, is shown in . a densitree [] is given in the electronic supplementary material, §4, to illustrate the variation in the posterior sample of trees. the beast 2 xml file for the best-fitting model, as well […]

PMCID: 5844911
PMID: 29523798
DOI: 10.1038/s41598-018-22478-4

[…] 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 […]


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

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