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

BMC Bioinformatics

Karl B Lopker¹  William Chen¹  Celia K C Churchill¹  M Sabrina Pankey¹  Roger Ngo¹  Markos A Alexandrou¹  Todd H Oakley¹ 

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

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

Others  :  1087560
DOI  :  10.1186/1471-2105-15-230

 received in 2013-12-01, accepted in 2014-04-29,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Oakley et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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