Intertwining phylogenetic trees and networks

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1 University of Massachusetts Boston, Boston, United States of America
2 Botany Department, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
3 Systematic Biology, Uppsala University, Uppsala, Sweden
4 University of Vienna, Vienna, Austria
DOI
10.7287/peerj.preprints.2054v1
Published
Accepted
Subject Areas
Computational Biology, Evolutionary Studies
Keywords
Networks, Exploratory Data Analysis, PHANGORN, R, Trees
Copyright
© 2016 Schliep et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Schliep K, Potts AA, Morrison DA, Grimm GW. 2016. Intertwining phylogenetic trees and networks. PeerJ Preprints 4:e2054v1

Abstract

The fields of phylogenetic tree and network inference have dramatically advanced in the last decade, but independently with few attempts to bridge them. Here we provide a framework, implemented in the phangorn library in R, to transfer information between trees and networks. This includes: 1) identifying and labelling equivalent tree branches and network edges, 2) transferring branch support to network edges, and 3) mapping bipartition support from a sample of trees (e.g. from bootstrapping or Bayesian inference) onto network edges. The ability to readily combine tree and network information should lead to more comprehensive evolutionary comparisons and conclusions.

Author Comment

This manuscript deals with a major update to the phangorn R library which focuses on objects and functions to transfer information between phylogenetic tree and network analyses. It has been submitted to a peer reviewed journal.