Minimal Support

Root

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Having the data defined as a set of objects, specialized storage methods are used to get direct access to the separate attributes of the selected objects, without having to touch the bulk of the data.

D4M

D4M attempts to combine the advantages of five distinct processing technologies (sparse linear algebra, associative arrays, fuzzy algebra, distributed arrays, and triple-store/NoSQL databases such as Hadoop HBase and Apache Accumulo) to provide a database and computation system that addresses the problems associated with Big Data. 

riboPicker

The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

At MSI, we provide a stand-alone version of the tool.  So the user must have some linux background to use this tool.

If you are not familiar with the command line, the developer also provides a web-version of the software at:

http://edwards.sdsu.edu/cgi-bin/ribopicker/ribopicker.cgi

MAKER

A portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.

Blast2Go

Is no longer supported at MSI. 

LIBSVM

LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.
 

MEGAN

MEGAN  (MEta-Genome ANalyzer) is a program for analyzing metagenomic datasets.  MEGAN can perform classification calculations, as well as allow for taxonomic visualization.

libxcb

The libxcb package provides an interface to the X Window System protocol, which replaces the current Xlib interface. Xlib can also use XCB as a transport layer, allowing software to make requests and receive responses with both.

librtfcomp

librtfcomp is a library to read and write compressed rtf files.

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