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DensiTree 2: Seeing Trees Through the Forest

Remco R. Bouckaert, Joseph Heled
doi: https://doi.org/10.1101/012401
Remco R. Bouckaert
University of Auckland
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  • For correspondence: r.bouckaert@auckland.ac.nz
Joseph Heled
University of Auckland
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  • For correspondence: r.bouckaert@auckland.ac.nz
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Abstract

Motivation Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip on a distributions over trees. Visualisation tools like DensiTree can give good intuition on tree distributions. It works by drawing all trees in the set transparently thus highlighting areas where the tree in the set agrees. In this way, both uncertainty in clade heights and uncertainty in topology can be visualised. In our experience, a vanilla DensiTree can turn out to be misleading in that it shows too much uncertainty due to wrongly ordering taxa or due to unlucky placement of internal nodes.

Results DensiTree is extended to allow visualisation of meta-data associated with branches such as population size and evolutionary rates. Furthermore, geographic locations of taxa can be shown on a map, making it easy to visually check there is some geographic pattern in a phylogeny. Taxa orderings have a large impact on the layout of the tree set, and advances have been made in finding better orderings resulting in significantly more informative visualisations. We also explored various methods for positioning internal nodes, which can improve the quality of the image. Together, these advances make it easier to comprehend distributions over trees.

Availability DensiTree is freely available from http://compevol.auckland.ac.nz/software/.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 08, 2014.
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DensiTree 2: Seeing Trees Through the Forest
Remco R. Bouckaert, Joseph Heled
bioRxiv 012401; doi: https://doi.org/10.1101/012401
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DensiTree 2: Seeing Trees Through the Forest
Remco R. Bouckaert, Joseph Heled
bioRxiv 012401; doi: https://doi.org/10.1101/012401

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