The 16S rRNA gene is widely used for taxonomic profiling of microbial ecosystems; and recent advances in sequencing chemistry have allowed extremely large numbers of sequences to be generated from minimal amounts of biological samples. Analysis speed and resolution of data to species-level taxa are two important factors in large-scale explorations of complex microbiomes using 16S sequencing. We present here new software, Phylogenetic Tools for Analysis of Species-level Taxa (PhyloToAST), that completely integrates with the QIIME pipeline to improve analysis speed, reduce primer bias (requiring two sequencing primers), enhance species-level analysis, and add new visualization tools. The code is free and open source, and can be accessed at http://phylotoast.org.

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Published in Scientific Reports, v. 6, article no. 29123, p. 1-9.

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These studies were funded through National Institute of Dental and Craniofacial Medicine (NIDCR) grant R01-DE022579. S.M.D. is supported by NIDCR grant T32-DE014320.

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All code for PhyloToAST is made available free and open source under the MIT license. The code is hosted on GitHub and may be downloaded at http://github.com/smdabdoub/phylotoast. Documentation of the API and all executable scripts can be found at http://docs.phylotoast.org.