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https://github.com/biocore/pynast

Software tool for aligning sequences to template alignment.

Proper citation: pynast (RRID:SCR_024189) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/patristic/

Software Java program for calculating patristic distances and graphically comparing the components of genetic change.

Proper citation: Patristic (RRID:SCR_024154) Copy   

•   Source: SciCrunch Registry

https://docs.igdiscover.se/en/stable/

Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: IgDiscover (RRID:SCR_024037) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/BOLT-LMM/

Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts.

Proper citation: BOLT-LMM (RRID:SCR_023978) Copy   

•   Source: SciCrunch Registry

https://quint-workflow.readthedocs.io/en/latest/QUINTintro.html

Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases.

Proper citation: QUINT (RRID:SCR_023856) Copy   

•   Source: SciCrunch Registry

https://www.gaain.org/

Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies.

Proper citation: Global Alzheimers Association Interaction Network (RRID:SCR_023699) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg-segment

Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.

Proper citation: Brainreg-segment (RRID:SCR_023853) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/iva

Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

Proper citation: IVA (RRID:SCR_024044) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-ut/PlasmidSeeker

Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.

Proper citation: PlasmidSeeker (RRID:SCR_024167) Copy   

•   Source: SciCrunch Registry

https://www.cancergenomeinterpreter.org/home

Platform that systematizes interpretation of cancer genomes and makes it automatic. Web tool to annotate genomic alterations and interpret their possible role in tumorigenesis and in response to anti cancer therapies. Used to support identification of tumor alterations that drive disease and/or which may be therapeutically actionable. Analyses mutations including single nucleotide changes and small insertions/deletions, copy number alterations including gene amplifications and deletions and translocations.

Proper citation: Cancer Genome Interpreter (RRID:SCR_023752) Copy   

•   Source: SciCrunch Registry

https://www.viewpoint.fr/product/zebrafish/cardiology/microzebralab

Software tool to extract cardiovascular parameters from transmitted light videos of zebrafish embryos or larvae. Used to investigate live and in non-invasive way scope of zebrafish larvae physiological parameters. Measures heartbeat and blood flow.

Proper citation: ViewPoint MicroZebraLab (RRID:SCR_023750) Copy   

•   Source: SciCrunch Registry

https://github.com/omnideconv/immunedeconv

Software R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.

Proper citation: Immunedeconv (RRID:SCR_023869) Copy   

•   Source: SciCrunch Registry

https://www.zeiss.com/microscopy/en/products/software/zeiss-zen-lite.html

Software tool for basic image acquisition and analysis. Zeiss ZEN microscopy software to control of axiocam microscope cameras, image transformation and measurements, image processing, image alignment for correlative microscopy, various visualization options.

Proper citation: Zeiss Zen Lite (RRID:SCR_023747) Copy   

•   Source: SciCrunch Registry

http://codonw.sourceforge.net

Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage.

Proper citation: CodonW (RRID:SCR_023989) Copy   

•   Source: SciCrunch Registry

https://www.bibliometrix.org/home/

Software R package for comprehensive science mapping analysis. Used for quantitative research in scientometrics and bibliometrics that includes all main bibliometric methods of analysis.

Proper citation: bibliometrix (RRID:SCR_023744) Copy   

•   Source: SciCrunch Registry

https://www.cubi.bihealth.org/software/varfish/

Web application for quality control, filtering, prioritization, analysis, and user based annotation of DNA variant data with focus on rare disease genetics. Comprehensive DNA variant analysis for diagnostics and research.

Proper citation: VarFish (RRID:SCR_023710) Copy   

•   Source: SciCrunch Registry

https://github.com/mskcc/lohhla

Software tool to evaluate HLA loss using next-generation sequencing data. Computational tool to determine HLA allele-specific copy number from sequencing data.

Proper citation: LOHHLA (RRID:SCR_023690) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/oncoboxlib/

Software library to calculate Pathways Activation Levels. It takes file that contains gene symbols in HGNC format, their expression levels for one or more samples and calculates PAL values for each pathway in each sample.

Proper citation: oncoboxlib (RRID:SCR_023722) Copy   

•   Source: SciCrunch Registry

https://github.com/Martinsos/edlib

Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.

Proper citation: Edlib (RRID:SCR_024078) Copy   

•   Source: SciCrunch Registry

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