Welcome to PhyloToAST documentation!

The PhyloToAST project is a collection of python scripts that modifies the original QIIME [1] pipeline:


by adding or modifying several steps (above in red) including support for PBS-based cluster-computing, multiple primer support [2], enhanced support for species-specific analysis, and additional visualization tools.



PhyloToAST is avaiable on the Python Package Index (PyPI), and can be easily installed with pip:

$ pip install phylotoast

Citing PhyloToAST

Dabdoub, S. M. et al. PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets. Sci. Rep. 6, 29123, 2016; doi: 10.1038/srep29123

Publications using PhyloToAST

Paropkari, A. D. et al. Smoking, Pregnancy and the Subgingival Microbiome. Sci. Rep. 6, 30388, 2016; doi: 10.1038/srep30388

Tsigarida and Dabdoub et al., The Influence of Smoking on the Peri-Implant Microbiome. Journal of Dental Research, 2015; doi: 10.1177/0022034515590581

Mason et al., The subgingival microbiome of clinically healthy current and never smokers. The ISME Journal, 2014; doi: 10.1038/ismej.2014.114

Dabdoub et al., Patient-specific Analysis of Periodontal and Peri-implant Microbiomes. Journal of Dental Research, 2013; doi: 10.1177/0022034513504950


[1]QIIME allows analysis of high-throughput community sequencing data. J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi: 10.1038/nmeth.f.303
[2]Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing. Kumar PS, Brooker MR, Dowd SE, Camerlengo T (2011) Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing. PLoS ONE 6(6): e20956. doi: 10.1371/journal.pone.0020956

Indices and tables