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http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry

https://prosite.expasy.org/scanprosite/

Web tool for detecting PROSITE signature matches in protein sequences.

Proper citation: ScanProsite (RRID:SCR_024425) Copy   

•   Source: SciCrunch Registry

https://github.com/PyWavelets/pywt

Software Python package for wavelet analysis.

Proper citation: PyWavelets (RRID:SCR_024421) Copy   

•   Source: SciCrunch Registry

https://sciex.com/products/software/proteinpilot-software

Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.

Proper citation: ProteinPilot (RRID:SCR_024414) Copy   

•   Source: SciCrunch Registry

https://github.com/paulgeeleher/pRRophetic

Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,

Proper citation: pRRophetic (RRID:SCR_024417) Copy   

•   Source: SciCrunch Registry

https://github.com/torognes/vsearch

Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data.

Proper citation: VSEARCH (RRID:SCR_024494) Copy   

•   Source: SciCrunch Registry

https://www.tomocube.com/product/tomostudio/

Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data.

Proper citation: TomoStudio (RRID:SCR_024498) Copy   

•   Source: SciCrunch Registry

https://www.photometrics.com/products/ocular

Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system.

Proper citation: Ocular (RRID:SCR_024490) Copy   

•   Source: SciCrunch Registry

https://github.com/SharonLutz/Umediation

Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding.

Proper citation: Umediation (RRID:SCR_024492) Copy   

•   Source: SciCrunch Registry

https://www.reading.ac.uk/bioinf/IntFOLD/

Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences.

Proper citation: IntFOLD (RRID:SCR_024523) Copy   

•   Source: SciCrunch Registry

https://www.malvernpanalytical.com/en/products/product-range/omnisec/accessories/omnisec-software

Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL.

Proper citation: OMNISEC (RRID:SCR_024485) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/software/phyldog/

Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously.

Proper citation: PHYLDOG (RRID:SCR_024487) Copy   

•   Source: SciCrunch Registry

https://github.com/chaoszhang/A-pro

Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.

Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy   

•   Source: SciCrunch Registry

https://kmplot.com/analysis/

Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.

Proper citation: Kaplan Meier Plotter (RRID:SCR_024521) Copy   

•   Source: SciCrunch Registry

https://www.jenoptik.com/products/cameras-and-imaging-modules/microscope-cameras/progres-usb-20-firewire/software-download-progres

Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.

Proper citation: ProgRes Capture Pro (RRID:SCR_024489) Copy   

•   Source: SciCrunch Registry

http://madoka.denglab.org/

Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.

Proper citation: MADOKA (RRID:SCR_024522) Copy   

•   Source: SciCrunch Registry

https://cab.spbu.ru/software/spades/

Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPAdes (RRID:SCR_000131) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

•   Source: SciCrunch Registry

http://www.mbfbioscience.com/stereo-investigator

Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology.

Proper citation: Stereo Investigator (RRID:SCR_002526) Copy   

•   Source: SciCrunch Registry