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https://github.com/harry-thorpe/piggy

Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).

Proper citation: Piggy (RRID:SCR_015941) Copy   

•   Source: SciCrunch Registry

http://www.gamgi.org/

Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter.

Proper citation: Gamgi (RRID:SCR_016116) Copy   

•   Source: SciCrunch Registry

http://disulfind.dsi.unifi.it/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.

Proper citation: DISULFIND (RRID:SCR_016072) Copy   

•   Source: SciCrunch Registry

https://github.com/boutiques/boutiques/

Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format.

Proper citation: Boutiques (RRID:SCR_016073) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/vboza/deepnano

Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.

Proper citation: DeepNano (RRID:SCR_016070) Copy   

•   Source: SciCrunch Registry

http://www.statsmodels.org/

Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html

Proper citation: statsmodel (RRID:SCR_016074) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.

Proper citation: Dotter (RRID:SCR_016080) Copy   

•   Source: SciCrunch Registry

http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gblocks (RRID:SCR_015945) Copy   

•   Source: SciCrunch Registry

http://www.treedyn.org/

Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TreeDyn (RRID:SCR_015946) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/FALCON

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

Proper citation: Falcon (RRID:SCR_016089) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/geocoding

Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.

Proper citation: geocoding (RRID:SCR_016007) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/SC3.html

Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.

Proper citation: SC3 (RRID:SCR_015953) Copy   

•   Source: SciCrunch Registry

https://github.com/haotianteng/Chiron

Software basecaller for Oxford Nanopore Technologies' sequencers.

Proper citation: Chiron (RRID:SCR_015950) Copy   

•   Source: SciCrunch Registry

http://www.hermit-reasoner.com/

Algorithm for a reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more.

Proper citation: HermiT OWL Reasoner (RRID:SCR_016006) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Exonerate (RRID:SCR_016088) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN

Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Proper citation: DOMALIGN (RRID:SCR_016085) Copy   

•   Source: SciCrunch Registry

https://github.com/osallou/cassiopee-c

Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.

Proper citation: Cassiopee (RRID:SCR_016056) Copy   

•   Source: SciCrunch Registry

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