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http://cdbfasta.sourceforge.net/

Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records.

Proper citation: Cdbfasta (RRID:SCR_016057) Copy   

•   Source: SciCrunch Registry
  

https://github.com/neurodroid/stimfit

Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.

Proper citation: Stimfit (RRID:SCR_016050) Copy   

•   Source: SciCrunch Registry
  

http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bio++ (RRID:SCR_016055) Copy   

•   Source: SciCrunch Registry
  

http://baderlab.org/Software/EnrichmentMap

Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together.

Proper citation: EnrichmentMap (RRID:SCR_016052) Copy   

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https://github.com/thegenemyers/DAZZ_DB

Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.

Proper citation: Dazzler (RRID:SCR_016069) Copy   

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http://scit.us/projects/dawg

Software application to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users.

Proper citation: Dawg (RRID:SCR_016068) Copy   

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http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

Proper citation: Clonalframe (RRID:SCR_016060) Copy   

•   Source: SciCrunch Registry
  

https://dazzlerblog.wordpress.com

Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers.

Proper citation: Daligner (RRID:SCR_016066) Copy   

•   Source: SciCrunch Registry
  

http://www.informatics.jax.org/home/strain

MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes.

Proper citation: Strains, SNPs and Polymorphisms (RRID:SCR_017518) Copy   

•   Source: SciCrunch Registry
  

http://www.informatics.jax.org/homology.shtml

MGI contains homology information for mouse, human, rat, chimp, dog and other species. Complete set of human, chimpanzee, rhesus macaque, dog, cattle, rat, chicken, western clawed frog and zebrafish Homology Classes for mouse genes. Report includes Chromosome and EntrezGene and OMIM IDs. Report of Human and Mouse Homology Classes sorted by HomoloGene ID includes associated nucleotide and protein sequences, Chromosome and OMIM IDs. Report of Human and Mouse Homology with phenotype annotations. Several additional MGI reports are available, including those for Gene Ontology, Phenotypes and Nomenclature.

Proper citation: Vertebrate Homology (RRID:SCR_017517) Copy   

•   Source: SciCrunch Registry
  

http://heimanlab.com/cut2.html

Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences. Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis.

Proper citation: Webcutter (RRID:SCR_017638) Copy   

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http://promoter.bx.psu.edu/hi-c/

Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: 3D Genome (RRID:SCR_017525) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/pubmed/17539361

Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people.

Proper citation: Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) Copy   

•   Source: SciCrunch Registry
  

http://carolina.imis.athena-innovation.gr/mirextra/

Software tool for analysis of expression data for microRNA function.

Proper citation: DIANA-mirExTra (RRID:SCR_017498) Copy   

•   Source: SciCrunch Registry
  

https://www.synapse.org/#!Synapse:syn11459638

Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3.

Proper citation: Multiple Myeloma survival predictor (RRID:SCR_017651) Copy   

•   Source: SciCrunch Registry
  

http://genelab.nasa.gov

Omics database for spaceflight experiments. Interactive, open access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Enables exploration of molecular network responses of terrestrial biology to space environment. Contains curated omics data, metadata and radiation dosimetry for model organisms. Supports standard guidelines for submission of datasets, MIAME for microarray, ENCODE Consortium Guidelines for RNA-seq and MIAPE Guidelines for proteomics.

Proper citation: GeneLab (RRID:SCR_017658) Copy   

•   Source: SciCrunch Registry
  

https://github.com/tanghaibao/mcscan

Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format.

Proper citation: MCScan (RRID:SCR_017650) Copy   

•   Source: SciCrunch Registry
  

https://epigenie.com/epigenetic-tools-and-databases/

Collection of epigenetic data browsers and repositories. Repository of epigenetics tools and databases by EpiGenie team.

Proper citation: Epigenie (RRID:SCR_017494) Copy   

•   Source: SciCrunch Registry
  

https://blobtools.readme.io/docs

Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants.

Proper citation: Blobtools (RRID:SCR_017618) Copy   

•   Source: SciCrunch Registry
  

https://umgear.org/

Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data.

Proper citation: gene Expression Analysis Resource (RRID:SCR_017467) Copy   

•   Source: SciCrunch Registry