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https://code.google.com/p/denovogui/

Software providing a user-friendly and lightweight graphical user interface for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics.

Proper citation: DeNovoGUI (RRID:SCR_012074) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/krux/

An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once.

Proper citation: kruX (RRID:SCR_012076) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snpratiotest/

Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.

Proper citation: SNP ratio test (RRID:SCR_012070) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/compomics-utilities/

A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics.

Proper citation: compomics-utilities (RRID:SCR_012073) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/campways/

Software that provides one-to-many alignments of reactions in a pair of metabolic pathways.

Proper citation: CAMPways (RRID:SCR_012072) Copy   

•   Source: SciCrunch Registry

http://toxtree.sourceforge.net/

A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach.

Proper citation: Toxtree (RRID:SCR_012086) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viewmol/

Software providing a graphical front end for computational chemistry programs.

Proper citation: Viewmol (RRID:SCR_012088) Copy   

•   Source: SciCrunch Registry

http://toxmatch.sourceforge.net/

A software tool to facilitate chemical similarity calculations.

Proper citation: Toxmatch (RRID:SCR_012087) Copy   

•   Source: SciCrunch Registry

http://qutemol.sourceforge.net/

Open source (GPL) software providing an interactive, high quality molecular visualization system.

Proper citation: QuteMol (RRID:SCR_012089) Copy   

•   Source: SciCrunch Registry

http://www2.unil.ch/cbg/index.php?title=ExpressionView

An R package that provides an interactive environment to explore biclusters identified in gene expression data.

Proper citation: ExpressionView (RRID:SCR_012004) Copy   

•   Source: SciCrunch Registry

http://bmi.osu.edu/hpc/software/bibench/index.html

A Python library designed to simplify biclustering tasks.

Proper citation: BiBench (RRID:SCR_012003) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/pride-asa-pipeline/

An open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database.

Proper citation: Pride-asap (RRID:SCR_012052) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/xtandem-parser/

An open-source Java library that parses X!Tandem XML result files into an easily accessible and fully functional object model.

Proper citation: XTandem Parser (RRID:SCR_012055) Copy   

•   Source: SciCrunch Registry

http://maltcms.sourceforge.net/users/features.html

An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics.

Proper citation: Maltcms (RRID:SCR_012057) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/pride-converter-2/

Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra.

Proper citation: PRIDE Converter 2 (RRID:SCR_012051) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/jmzreader/

A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML.

Proper citation: jmzReader (RRID:SCR_012050) Copy   

•   Source: SciCrunch Registry

http://insilicogenome.sourceforge.net/

A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations.

Proper citation: FIGG (RRID:SCR_012064) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/diyg/

A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences.

Proper citation: DIYA (RRID:SCR_012066) Copy   

•   Source: SciCrunch Registry

http://fastphylo.sourceforge.net/

A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix.

Proper citation: Fastphylo (RRID:SCR_012068) Copy   

•   Source: SciCrunch Registry

http://mrbayes.sourceforge.net/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Proper citation: MrBayes (RRID:SCR_012067) Copy   

•   Source: SciCrunch Registry