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.



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

Show Project


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

Show Project


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

Show Project


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

Show Project


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

Show Project


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

Show Project

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.

Show Project

JCVI Primer Designer

High throughput PCR primer design software.

Show Project


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

Show Project


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

Show Project


JCVI Cloud BioLinux

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

Show Project

Metagenomics Analysis


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

Show Project



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

Show Project