Tools   Select Another Resource Report Type

https://github.com/GATB/MindTheGap

Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.

Proper citation: MindTheGap (RRID:SCR_024115) Copy   

•   Source: SciCrunch Registry

https://jydu.github.io/maffilter/

Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.

Proper citation: MafFilter (RRID:SCR_024105) Copy   

•   Source: SciCrunch Registry

https://sparta.readthedocs.io/en/latest/

Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.

Proper citation: sparta (RRID:SCR_024349) Copy   

•   Source: SciCrunch Registry

http://maude.cs.illinois.edu/w/index.php/The_Maude_System

Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation.

Proper citation: Maude (RRID:SCR_024108) Copy   

•   Source: SciCrunch Registry

https://github.com/Pas-Kapli/mptp

Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.

Proper citation: mPTP (RRID:SCR_024121) Copy   

•   Source: SciCrunch Registry

https://github.com/bartongroup/yanosim

Software tool as read simulator for nanopore DRS datasets.

Proper citation: Yanosim (RRID:SCR_024363) Copy   

•   Source: SciCrunch Registry

http://ugovaretto.github.io/molekel/

Open source multi platform molecular visualization program.

Proper citation: Molekel (RRID:SCR_024122) Copy   

•   Source: SciCrunch Registry

https://www.mrtrix.org/

Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.

Proper citation: MRtrix3 (RRID:SCR_024123) Copy   

•   Source: SciCrunch Registry

https://mia.sourceforge.net/

Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality.

Proper citation: MIA (RRID:SCR_024081) Copy   

•   Source: SciCrunch Registry

http://www.ccmb.med.umich.edu/ccdu/SNPAAMapper

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take

Proper citation: SNPAAMapper (RRID:SCR_002012) 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://sourceforge.net/projects/skewer/

Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.

Proper citation: skewer (RRID:SCR_001151) Copy   

•   Source: SciCrunch Registry

https://github.com/princelab/mspire-simulator

A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components.

Proper citation: Mspire-Simulator (RRID:SCR_001431) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/openwalnut/

Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows.

Proper citation: OpenWalnut (RRID:SCR_014157) Copy   

•   Source: SciCrunch Registry

http://copasi.org/

Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization.

Proper citation: COPASI (RRID:SCR_014260) Copy   

•   Source: SciCrunch Registry

http://www.cyana.org/wiki/index.php/Main_Page

Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution.

Proper citation: CYANA (RRID:SCR_014229) Copy   

•   Source: SciCrunch Registry

http://scratch.proteomics.ics.uci.edu/index.html

Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.

Proper citation: SCRATCH (RRID:SCR_014291) Copy   

•   Source: SciCrunch Registry

http://sysbio.rnet.missouri.edu/multicom_toolbox/NNCon%201.0.html

Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.

Proper citation: NNcon (RRID:SCR_014292) 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://shelx.uni-ac.gwdg.de/SHELX/

A set of software programs that utilizes dual spaces algorithms for the determination of small and macromolecular crystal structures by single crystal X-ray and neutron diffraction. Libraries, extra files and environment variables are not required for the executables. SHELX is intended to be run on a command prompt but may be called from GUIs such as shelXle, Olex2, Oscail or WinGX, or hkl2map., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SHELX (RRID:SCR_014220) Copy   

•   Source: SciCrunch Registry