FOCUS, an innovative and agile model to profile and report organisms present in metagenomic samples based on composition usage without sequence length dependencies.

Project site


PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. It generates summary statistics of your sequences in graphical and tabular format. It is easily configurable and provides a user-friendly interface.

Project site

The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

project site


PhiSpy: A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies

project site


Phenotypic microarray assay analysis for 96-well multi-plate spectrophotometers.

project repo


PHACTS can be used to quickly classify the lifestyle of a phage. All that is needed is the proteome of the phage to be classified and PHACTS will predict the lifestyle of that phage and return a confidence value for that prediction.

project site 


The PhAnToMe—PHage ANnotation TOols and MEthods—project was launched withNSF funding to establish a phage annotation database, a visual programming interface (Phage BioBike), and a rapid annotation pipeline for phage genomes (PhiRAST—phage Rapid Annotation Using Subsystem Technology).

The Phantome project consists of many components: our PhageSeed database is an integration of all sequenced phage genomes, and also provides access to prophages, bacterial genomes, and more. The PhiRAST software that we are developing with colleagues at Argonne National Labs and the Fellowship for Interpretation of Genomesallows rapid annotation of phage genomes from a fasta DNA sequence file.PhageBioBike provides a graphical programming language for accessing data in thePhageSeed database, providing a more robust way to access the data.

Project site