Tools   Select Another Resource Report Type

http://www.qsrinternational.com/nvivo-product

Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed.

Proper citation: NVivo (RRID:SCR_014802) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/prottest_server.html

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProtTest (RRID:SCR_014628) Copy   

•   Source: SciCrunch Registry

http://iupred.enzim.hu/

A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence.

Proper citation: IUPRED (RRID:SCR_014632) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

Proper citation: FastQC (RRID:SCR_014583) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET

Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces.

Proper citation: Brain Extraction Tool (RRID:SCR_014586) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

Proper citation: Bowtie 2 (RRID:SCR_016368) Copy   

•   Source: SciCrunch Registry

http://spider.science.strath.ac.uk/sipbs/software_ses.htm

Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection.

Proper citation: WinWCP (RRID:SCR_014713) Copy   

•   Source: SciCrunch Registry

http://paup.sc.fsu.edu

Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis.

Proper citation: PAUP (RRID:SCR_014931) Copy   

•   Source: SciCrunch Registry

http://www.statgraphics.com/download-statgraphics-centurion-xvii

Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers.

Proper citation: Statgraphics Centurion (RRID:SCR_015248) Copy   

•   Source: SciCrunch Registry

https://www.metaboanalyst.ca/

Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.

Proper citation: MetaboAnalyst (RRID:SCR_015539) Copy   

•   Source: SciCrunch Registry

http://www.thegpm.org/tandem/

Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences.

Proper citation: X!Tandem (RRID:SCR_015645) Copy   

•   Source: SciCrunch Registry

https://jasp-stats.org/

Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests.

Proper citation: JASP (RRID:SCR_015823) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/mcode

Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks.

Proper citation: MCODE (RRID:SCR_015828) Copy   

•   Source: SciCrunch Registry

https://www.github.com/arq5x/poretools

Software toolkit for analyzing nanopore sequence data.

Proper citation: Poretools (RRID:SCR_015879) Copy   

•   Source: SciCrunch Registry

http://galaxyproject.org/

Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.

Proper citation: Galaxy (RRID:SCR_006281) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/FLASH/

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

Proper citation: FLASH (RRID:SCR_005531) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/standard-RAxML

Software program for phylogenetic analyses of large datasets under maximum likelihood.

Proper citation: RAxML (RRID:SCR_006086) Copy   

•   Source: SciCrunch Registry

https://gmod.org/wiki/CMap.1

Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)

Proper citation: CMAP (RRID:SCR_009034) Copy   

•   Source: SciCrunch Registry

http://bioinf.cs.ucl.ac.uk/psipred/

Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences.

Proper citation: PSIPRED (RRID:SCR_010246) Copy   

•   Source: SciCrunch Registry

http://www.sigmaplot.com/products/sigmaplot/sigmaplot-details.php

Software tool for data graphing and analysis by Systat Software, Inc.

Proper citation: SigmaStat (RRID:SCR_010285) Copy   

•   Source: SciCrunch Registry