Abstract
BackgroundPhylogenetic 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.ResultsWe 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/).ConclusionsOsiris can serve as a foundation for other phylogenomic and phylogenetic tool development within the Galaxy platform.
Highlights
Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research
New analysis paradigms are available, like BEAST XML [1], phyloXML [2], NeXML [3], reproducibility of phylogenetic analyses is still hampered by a lack of standardization of analytical programs, which have varied authors, different requirements, and use multiple file formats
Implementation Here we describe our development of a suite of tools we collectively refer to as Osiris, which allow extensive phylogenetic analyses within the Galaxy bioinformatics platform
Summary
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 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/)
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