Search Software

  • Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data.

  • BioPerl is a toolkit of Perl modules useful for building bioinformatics programs in perl.

  • Read SAM/BAM databases within Bioperl. http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm

  • Chenomx NMR suite is an integrated suite of tools that allow you to easily identify and quantify metabolites in NMR spectra. The following products make up Chenomx NMR Suite:

  • CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. Publication: http://www.ncbi.nlm.nih.gov/pubmed/21666668

     

  • ea-utils provides command-line tools for processing biological sequencing data using methods such as barcode demultiplexing, adapter trimming, etc.  It was primarily written to support an Illumina based pipeline - but should work with any FASTQs.

  • Galaxy is a web-based platform for data intensive biomedical research.  Anyone with an account at MSI can access the Galaxy server at galaxy.msi.umn.edu

  • The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary.  It is based on a C library named “libgenometools” which consists of several modules.

  • GraphClust can be used for structural clustering of RNA sequences. Especially it can be used for clustering of very large dataset with thousands of RNAs.

    http://www.bioinf.uni-freiburg.de/Software/GraphClust/

  • GraphPad Prism from GraphPad Software is a combination of basic biostatistics, curve fitting and scientific graphing in one comprehensive program.

  • HMMER is an implementation of profile hidden Markov model (HMM) methods for sensitive database searches using multiple sequence alignments as queries.  HMMER takes a multiple sequence alignment as input.
  • JMP

    JMP is a statistical discovery software. It is the SAS product designed for dynamic data visualization on the desktop. It links statistics with graphics and makes users data accessible easily in many ways.

  • "LocaRNA is a package of tools for producing fast and high-quality pairwise and multiple alignment of RNA sequences. It uses a complex RNA energy model for simultaneous folding and sequence/structure alignment of the RNAs.

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

  • NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons.

  • R

    R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible.

  • "RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler."

  • "RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs."

  • SAS

    SAS is a scalable, integrated software environment and a flexible and extensible programming language designed for data access, data manipulation, and data analysis. It offers data management and predictive analytic capabilities, data mining process, drug discovery solutions, and much more.

  • Software which uses a clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

  • Stata is an integrated statistical package that provides extensive functionality for data analysis, data management, and graphics.

  • The program structure is a free software package for using multi-locus genotype data to investigate population structure.