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https://github.com/adamallo/SimPhy

Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees.

Proper citation: SimPhy (RRID:SCR_024501) Copy   

•   Source: SciCrunch Registry

http://mutationassessor.org/r3/

Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Mutation Assessor (RRID:SCR_024502) Copy   

•   Source: SciCrunch Registry

https://github.com/pinellolab/CRISPResso2

Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.

Proper citation: CRISPResso2 (RRID:SCR_024503) Copy   

•   Source: SciCrunch Registry

https://silebat.github.io/FSK-Lab/openbugs.html

Software for analysing complex statistical models using Markov chain Monte Carlo methods.

Proper citation: OpenBUGS (RRID:SCR_024488) Copy   

•   Source: SciCrunch Registry

https://github.com/bzhanglab/AutoRT/

Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides.

Proper citation: AutoRT (RRID:SCR_024513) Copy   

•   Source: SciCrunch Registry

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

Web server for the global and local quality estimation of 3D protein models

Proper citation: ModFOLD (RRID:SCR_024518) Copy   

•   Source: SciCrunch Registry

http://metscape.ncibi.org

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

Proper citation: Metscape (RRID:SCR_014687) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/software/minc/

A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction.

Proper citation: MINC (RRID:SCR_002391) Copy   

•   Source: SciCrunch Registry

https://www.openepi.com/Menu/OE_Menu.htm

Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection.

Proper citation: OpenEpi (RRID:SCR_021913) Copy   

•   Source: SciCrunch Registry

http://www.project-redcap.org/

Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.

Proper citation: REDCap (RRID:SCR_003445) Copy   

•   Source: SciCrunch Registry

http://www.vmatch.de/

Software tool for efficiently solving large scale sequence matching tasks.

Proper citation: Vmatch (RRID:SCR_018968) Copy   

•   Source: SciCrunch Registry

http://www.mcbainsystems.com/Leica_QWin.php

Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional.

Proper citation: Leica QWin (RRID:SCR_018940) Copy   

•   Source: SciCrunch Registry

https://past.en.lo4d.com/windows

Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy.

Proper citation: PAST (RRID:SCR_019129) Copy   

•   Source: SciCrunch Registry

http://msquant.sourceforge.net/

Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine.

Proper citation: MSQuant (RRID:SCR_019206) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/biomaRt/

Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.

Proper citation: biomaRt (RRID:SCR_019214) 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

https://www.vicon.com/products/software/nexus

Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment.

Proper citation: Nexus (RRID:SCR_015001) 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.statmodel.com

Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data.

Proper citation: MPlus (RRID:SCR_015578) 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