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http://www.softgenetics.com/GeneMarker.php

Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software.

Proper citation: GeneMarker (RRID:SCR_015661) Copy   

•   Source: SciCrunch Registry

http://phobius.sbc.su.se/

Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states.

Proper citation: Phobius (RRID:SCR_015643) Copy   

•   Source: SciCrunch Registry

https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

Proper citation: Genesis (RRID:SCR_015775) Copy   

•   Source: SciCrunch Registry

http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gblocks (RRID:SCR_015945) Copy   

•   Source: SciCrunch Registry

https://github.com/CAMI-challenge/AMBER

Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.

Proper citation: AMBER (RRID:SCR_016151) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/MACH/download/

QTL analysis based on imputed dosages/posterior_probabilities.

Proper citation: MACH (RRID:SCR_009621) Copy   

•   Source: SciCrunch Registry

http://weblogo.berkeley.edu

Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator.

Proper citation: WEBLOGO (RRID:SCR_010236) Copy   

•   Source: SciCrunch Registry

http://www.geneious.com/

Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.

Proper citation: Geneious (RRID:SCR_010519) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.

Proper citation: ABySS (RRID:SCR_010709) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry

https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE

Software tool for flow and image cytometry data analysis by De Novo Software company.

Proper citation: FCS Express (RRID:SCR_016431) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html

Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.

Proper citation: BLASTClust (RRID:SCR_016641) Copy   

•   Source: SciCrunch Registry

http://grigoriefflab.janelia.org/ctffind4

Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.

Proper citation: CTFFIND (RRID:SCR_016732) Copy   

•   Source: SciCrunch Registry

http://www.bio-rad.com/en-eh/product/cfx-manager-software

Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CFX Manager (RRID:SCR_017251) Copy   

•   Source: SciCrunch Registry

http://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html

Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program.

Proper citation: RNAstructure (RRID:SCR_017216) Copy   

•   Source: SciCrunch Registry

https://automeris.io/WebPlotDigitizer/

Web based tool to extract data from plots, images, and maps. HTML5 based online tool to extract numerical data from plot images. Used to reverse engineer images of data visualizations to extract underlying numerical data.

Proper citation: WebPlotDigitizer (RRID:SCR_013996) Copy   

•   Source: SciCrunch Registry

https://www.phenix-online.org/documentation/reference/phaser.html

Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods.

Proper citation: Phaser (RRID:SCR_014219) Copy   

•   Source: SciCrunch Registry

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

Proper citation: Coot (RRID:SCR_014222) Copy   

•   Source: SciCrunch Registry

http://www.malvern.com/en/products/technology/nanoparticle-tracking-analysis/

Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation.

Proper citation: Nanoparticle Tracking Analysis (RRID:SCR_014239) Copy   

•   Source: SciCrunch Registry

http://www.jmp.com/en_us/software/jmp.html

Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design.

Proper citation: JMP (RRID:SCR_014242) Copy   

•   Source: SciCrunch Registry