Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
- 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
- 2015. Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. PeerJ PrePrints 3:e1106v1 https://doi.org/10.7287/peerj.preprints.1106v1
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.