A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
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 transpare...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-03-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/3058.pdf |
| _version_ | 1797418972516188160 |
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| author | Benjamin D. Redelings Mark T. Holder |
| author_facet | Benjamin D. Redelings Mark T. Holder |
| author_sort | Benjamin D. Redelings |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T06:40:43Z |
| format | Article |
| id | doaj.art-dc102ef28b074cefbc89e4c119a6ae57 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:40:43Z |
| publishDate | 2017-03-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-dc102ef28b074cefbc89e4c119a6ae572023-12-03T10:51:37ZengPeerJ Inc.PeerJ2167-83592017-03-015e305810.7717/peerj.3058A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of speciesBenjamin D. Redelings0Mark T. Holder1Department of Biology, Duke University, Durham, NC, United StatesDepartment of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United StatesWe 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.https://peerj.com/articles/3058.pdfSupertreePhylogeneticsTaxonomySoftwareTree of life |
| spellingShingle | Benjamin D. Redelings Mark T. Holder A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species PeerJ Supertree Phylogenetics Taxonomy Software Tree of life |
| title | A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species |
| title_full | A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species |
| title_fullStr | A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species |
| title_full_unstemmed | A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species |
| title_short | A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species |
| title_sort | supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species |
| topic | Supertree Phylogenetics Taxonomy Software Tree of life |
| url | https://peerj.com/articles/3058.pdf |
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