Tools   Select Another Resource Report Type

https://cran.r-project.org/web/packages/igraph/

Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.

Proper citation: igraph (RRID:SCR_019225) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.

Proper citation: PROCHECK (RRID:SCR_019043) Copy   

•   Source: SciCrunch Registry

http://www.biosoft.com/w/calcusyn.htm

Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools.

Proper citation: CalcuSyn (RRID:SCR_020251) Copy   

•   Source: SciCrunch Registry

https://www.miltenyibiotec.com/products/macs-flow-cytometry/software/flowlogic-software.html

Software tool for flow cytometry data analysis by Miltenyi Biotec.

Proper citation: Flowlogic (RRID:SCR_020942) Copy   

•   Source: SciCrunch Registry

https://gradepro.org/

Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables.

Proper citation: GRADEpro (RRID:SCR_021308) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/jcvi/

Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Proper citation: jcvi (RRID:SCR_021641) Copy   

•   Source: SciCrunch Registry

https://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry

http://www.prisma-statement.org/

Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.

Proper citation: PRISMA (RRID:SCR_018721) Copy   

•   Source: SciCrunch Registry

https://github.com/blackrim/phyutility

Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.

Proper citation: Phyutility (RRID:SCR_018545) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/software/elda/

Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.

Proper citation: ELDA (RRID:SCR_018933) 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

http://clustalw.ddbj.nig.ac.jp/index.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan.

Proper citation: ClustalW (RRID:SCR_017277) 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

http://www.sanger.ac.uk/resources/software/alien_hunter/

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.

Proper citation: Alien hunter (RRID:SCR_004575) Copy   

•   Source: SciCrunch Registry

Issue

https://reich.hms.harvard.edu/software

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.

Proper citation: Eigensoft (RRID:SCR_004965) Copy   

•   Source: SciCrunch Registry

http://www.utexas.edu

A major university

Proper citation: University of Texas at Austin; Texas; USA (RRID:SCR_005900) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.oxfordjournals.org/content/early/2012/05/10/bioinformatics.bts271.full.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. The method employs a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, whilst leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. The method has superior accuracy and sensitivity on impure samples compared to approaches based on either diploid genotype likelihoods or general allele-frequency tests.

Proper citation: Strelka (RRID:SCR_005109) Copy   

•   Source: SciCrunch Registry

http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV/

Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.

Proper citation: MetaPSICOV (RRID:SCR_024517) Copy   

•   Source: SciCrunch Registry

https://www.sqlite.org/index.html

Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.

Proper citation: SQLite (RRID:SCR_017672) Copy   

•   Source: SciCrunch Registry