- 【Updated on May 12, 2025】 Integration of CiNii Dissertations and CiNii Books into CiNii Research
- Trial version of CiNii Research Knowledge Graph Search feature is available on CiNii Labs
- 【Updated on June 30, 2025】Suspension and deletion of data provided by Nikkei BP
- Regarding the recording of “Research Data” and “Evidence Data”
DensiTree: making sense of sets of phylogenetic trees
-
- Remco R. Bouckaert
- Department of Computer Science, Auckland University
Search this article
Description
<jats:title>Abstract</jats:title> <jats:p>Motivation: Bayesian analysis through programs like BEAST (Drummond and Rumbaut, 2007) and MrBayes (Huelsenbeck et al., 2001) provides a powerful method for reconstruction of evolutionary relationships. One of the benefits of Bayesian methods is that well-founded estimates of uncertainty in models can be made available. So, for example, not only the mean time of a most recent common ancestor (tMRCA) is estimated, but also the spread. This distribution over model space is represented by a set of trees, which can be rather large and difficult to interpret. DensiTree is a tool that helps navigating these sets of trees.</jats:p> <jats:p>Results: The main idea behind DensiTree is to draw all trees in the set transparently. As a result, areas where a lot of the trees agree in topology and branch lengths show up as highly colored areas, while areas with little agreement show up as webs. This makes it possible to quickly get an impression of properties of the tree set such as well-supported clades, distribution of tMRCA and areas of topological uncertainty. Thus, DensiTree provides a quick method for qualitative analysis of tree sets.</jats:p> <jats:p>Availability: DensiTree is freely available from http://compevol.auckland.ac.nz/software/DensiTree/. The program is licensed under GPL and source code is available.</jats:p> <jats:p>Contact: remco@cs.auckland.ac.nz</jats:p>
Journal
-
- Bioinformatics
-
Bioinformatics 26 (10), 1372-1373, 2010-03-12
Oxford University Press (OUP)
- Tweet
Details 詳細情報について
-
- CRID
- 1364233269203698688
-
- ISSN
- 13674811
- 13674803
-
- Data Source
-
- Crossref