Pique – Fast & accurate ChIP-Seq peak finder specifically for microbial data



MotifCatcher– Sensitive Monte Carlo-based motif-finding. The link will forward you to the MATLAB File Exchange for easy download. Supplementary scripts and data for MotifCatcher can be found here.


JContextExplorer 3.0

A Tree-based approach to facilitate cross-species genomic context comparison.

Download JAR

Download ZIP

JContextExplorer is a genomes delivery platform. If you like the convenient, intuitive interface JContextExplorer provides for accessing genomes data sets, contact Marc Facciotti ( and we will happily add your genome set to our software.


(1A) Click the Download JAR link.
This will download the executable .JAR (java archive file) onto your computer.
If this is successful, you may click on the downloaded .JAR file to launch, or from a command line
launch the jar using

java -jar [path-to-jar]/JContextExplorer30.jar

If you are working with a large genome set (for example, the haloarchaea), we recommend launching JContextExplorer with a larger maximum heap size. To do that, type

java -Xmx1024M -jar [path-to-jar]/JContextExplorer30.jar

If this still does not work, proceed to step (1C).

(1B) Click the Download ZIP link.
This zipped directory contains the .JAR file. Unzip the directory, and follow the instructions
described in (1B) to launch the program from the .JAR

If you are still unable to get JContextExplorer to work, please see the Troubleshooting section below.

(2) Start using the program.
Check out the User’s Manual (linked below) and video tutorials (also linked below) to get started.

JContextExplorer User Manual: As Word Document or As PDF

How to Process Your Genome Sets to Import into JContextExplorer: .zip File

Video Tutorials

01 Introduction of JContextExplorer
This video covers the basics, from importing a Genomic Set to performing basic searches and drawing context trees.

02 Advanced Features of JContextExplorer
This tutorial highlights some of the advanced features available in the JContextExplorer software platform.


If you’re working on a Mac OS X 10.6 or lower, JCE may not work. This may be because of your version of Java, or your security settings. You can change your security settings by navigating to your Applications folder -> Utilies -> Java Preferences, or to Apple -> System Preferences -> Other -> Java. If you version of Java is the culprit, this may offer some help: Help for Mac Users. If these steps still do not work, you may launch JContextExplorer from the ‘Download’ link shown above. In that case, you may need to change your Security settings to allow for non Mac App Store programs to run. To change these security settings, navigate to System Preferences -> Security and Privacy, and in the ‘General’ tab, under ‘Allow applications downloaded from:’, select ‘Anywhere’.

Available Genome Sets and Associated Files

Haloarchaea Download
rpoB”-based phylogenetic tree Download
motif-based computationally predicted promoters Download
computationally predicted CRISPRs Download

Chloroviruses Download

Mimiviruses Download

Myxococcus Download

Build Your Own Genome Set

JCE Homology Cluster Pipeline: Download

JCE Homology Cluster Pipeline Instructions: PDF

Source Code

Github Repository: PMSeitzer/JContextExplorer

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