Tools   Select Another Resource Report Type

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

http://sourceforge.net/projects/mmax2/

A GUI-based text annotation tool for creating and visualizing annotations.

Proper citation: MMAX2 (RRID:SCR_012100) Copy   

•   Source: SciCrunch Registry

http://ipapers.sourceforge.net/iPapers.html

Software application that manages many PDF files of articles, whose information can be obtained by PubMed.

Proper citation: iPapers (RRID:SCR_012103) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phylotreepruner/

A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods.

Proper citation: PhyloTreePruner (RRID:SCR_012069) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/coperead/

An efficient software tool to connect overlapping pair-end reads using k-mer frequencies.

Proper citation: Connecting Overlapped Pair-End reads (RRID:SCR_012102) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/raspnmr/

Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy.

Proper citation: RASP (RRID:SCR_012062) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gsim/

Free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.

Proper citation: GSim (RRID:SCR_012061) Copy   

•   Source: SciCrunch Registry

http://cat.princeton.edu/

A software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs).

Proper citation: CCAT (Combinatorial Code Analysis Tool) (RRID:SCR_012028) Copy   

•   Source: SciCrunch Registry

http://cractools.gforge.inria.fr/softwares/digitagct

Software that combines digital gene expression (DGE) tags, RNA-Seq, tiling array expression data and species-comparison to explore new transcriptional regions and their specific biological features, particularly tissue expression or conservation.

Proper citation: digitagCT (RRID:SCR_012027) Copy   

•   Source: SciCrunch Registry