Software Tools

JCVI was one of three Genomic Centers for Infectious Diseases (GCID) funded by the National Institute for Allergy and Infectious Diseases (NIAID) to develop basic knowledge of infectious disease biology through the application of DNA sequencing, genotyping and comparative genome analysis. Throughout the history of GCID, and its predecessor contracts, the program has pioneered many strategies and approaches for the interrogation of genomics-based data. The program developed a suite of pipelines and tools, which are constantly updated and adapted to address new organisms, accommodate data from new sequencing platforms, and for the investigation of new types of scientific questions. All tools developed under the GCID are publicly available and open source. While JCVI is no longer funded through this NIAID funded program, the expertise and knowledge gained from it continues to flourish and enhance the greater scientific community.



Homology-based viral gene finder, predicting both proteins and mature peptides.


PanACEA is a tool for Pan-Genome visualization, which utilizes locally-computed interactive web-pages to view ordered pan-genome data.


Phage_Finder is a heuristic computer program written in PERL to identify prophage regions within bacterial genomes.


A custom sequence locus typer for classifying microbial genotypic and phenotypic attributes.


An R-package for selecting representative genomes using Gaussian mixture models.


Collection of Java, Perl, and PHP tools supporting high-throughput sample sequencing, metadata, analysis, and reports for viral projects.

DNA Barcode Deconvolution

This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid.

JCVI Primer Designer

High throughput PCR primer design software.


Java framework for reading, writing, analyzing and manipulating sequence and assembly data.


PanOCT is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains.


JCVI Cloud BioLinux

Enabling scientists to quickly provision cloud-based bioinformatics platforms such as Amazon EC2 and Eucalyptus.

Metagenomics Analysis


Metagenomics Reports (METAREP) is an open source tool for high-performance comparative metagenomics.



OMeta is a data driven application that can be configured to track project, study, sample, experiment, or clinical data.