Abstract:
:We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree. We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies. This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project's "synthetic tree" starting at version 5. This software pipeline is called "propinquity". It relies heavily on "otcetera"-a set of C++ tools to perform most of the steps of the pipeline. All of the components are free software and are available on GitHub.
journal_name
PeerJjournal_title
PeerJauthors
Redelings BD,Holder MTdoi
10.7717/peerj.3058subject
Has Abstractpub_date
2017-03-01 00:00:00pages
e3058issn
2167-8359pii
3058journal_volume
5pub_type
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