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Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

Todd H Oakley*, Markos A Alexandrou, Roger Ngo, M Sabrina Pankey, Celia K C Churchill, William Chen and Karl B Lopker

Author Affiliations

Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA

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BMC Bioinformatics 2014, 15:230  doi:10.1186/1471-2105-15-230

Published: 2 July 2014

Abstract

Background

Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies. Therefore, there is an urgent need for accessible, modular, and sharable tools for phylogenetic analysis.

Results

We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris. Osiris and Galaxy provide a sharable, standardized, modular user interface, and the ability to easily create complex workflows using a graphical interface. Osiris enables all aspects of phylogenetic analysis within Galaxy, including de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic tree estimation, and post-tree comparative analysis. The open source files are available on in the Bitbucket public repository and many of the tools are demonstrated on a public web server (http://galaxy-dev.cnsi.ucsb.edu/osiris/ webcite).

Conclusions

Osiris can serve as a foundation for other phylogenomic and phylogenetic tool development within the Galaxy platform.

Keywords:
Phylogenomics; Phylogenetics; Galaxy; Orthology; Assembly; Next-generation sequence analysis; Sequence alignment; Tree estimation