Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

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1 Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, United States of America
2 Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
3 Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
4 Department of Computer Science and BioFrontiers Institute, University of Colorado at Boulder, Boulder, Colorado, United States of America
5 Department of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, United States of America
6 Department of Biology, San Diego State University, San Diego, California, United States of America
DOI
10.7287/peerj.preprints.1106v1
Published
Accepted
Subject Areas
Bioinformatics, Microbiology
Keywords
fungal diversity, phylogenetics, environmental microbiology, microbial diversity, ITS, UniFrac, software, bioinformatics
Copyright
© 2015 Fouquier 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
Fouquier J, Rideout JR, Bolyen E, Chase JH, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST. 2015. Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. PeerJ PrePrints 3:e1106v1

Abstract

Ghost-tree is a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach uses one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families) as a “foundation” phylogeny. A second, more rapidly evolving genetic marker is then used to build “extension” phylogenies for more closely related organisms (e.g., fungal species or strains) that are then grafted on to the foundation tree by mapping taxonomic names. We apply ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. The result is a phylogenetic tree, compatible with the commonly used UNITE fungal database, that supports phylogenetic diversity analysis (e.g., UniFrac) of fungal communities profiled using ITS markers. Availability: ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.

Author Comment

This is a preprint to be submitted for a special issue in the journal Microbiome.