Pique

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

MotifCatcher

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 2.0 – Official Release May 22, 2013

A Tree-based approach to facilitate cross-species genomic context comparison.
This version has a more classic look and feel.
JCE now starts with the main window, and features a central menu bar. Data may be loaded in one or more genome sets, which the user may switch between. In addition to data import via files, data may now be directly imported from NCBI’s online database, or streamed in from one or more pre-existing genome sets available on this page.

 

For a complete description of the new features, improvements, and bug fixes, please see the updated manual and tutorial videos.

 

Version 2 of the software is now complete, however the tutorial videos and user’s manual have not yet been updated.

JContextExplorer

 

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

JContextExplorer User Manual: As Word Document or As PDF

Supplemental data set: 22 Alpha and Gamma proteobacteria Download

Source Code: GitHub

Video Tutorials:
Playlist: Introduction, Retrieval, and Usage
01 Introduction
02 Retrieval
03 Usage

Playlist: Updates Nov 17, 2012 and Context Tree Export
04 Updates Nov. 17, 2012
05 Context Tree Export