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https://github.com/bbuchfink/diamond

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

Proper citation: DIAMOND (RRID:SCR_016071) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry

http://www.csd.uwo.ca/~ilie/E-MEM/

Software for an efficient maximal exact match (MEM) computation program that does not use full text indexes, uses less space and is amenable to parallelization. It can be used as a stand alone application or a drop-in replacement for MUMmer3 system for rapidly aligning entire genomes.

Proper citation: E-mem (RRID:SCR_016081) Copy   

•   Source: SciCrunch Registry

http://genometools.org

Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization.

Proper citation: GenomeTools (RRID:SCR_016120) Copy   

•   Source: SciCrunch Registry

http://sanger-pathogens.github.io/circlator/

Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes.

Proper citation: Circlator (RRID:SCR_016058) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.hungry.com/clearcut/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Clearcut (RRID:SCR_016059) Copy   

•   Source: SciCrunch Registry

https://www.wyatt.com/products/software/astra.html

Software for the characterization of macromolecules and nanoparticles via multi-angle and dynamic light scattering. It simplifies MALS and DLS analysis for assessment of molar mass, size, conformation, conjugation, and other essential physical parameters.

Proper citation: ASTRA (RRID:SCR_016255) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metagenomics/

Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.

Proper citation: MGnify (RRID:SCR_016429) Copy   

•   Source: SciCrunch Registry

https://github.com/maplesond/portcullis

Software for filtering invalid Splice junctions from pre-aligned RNA-seq data. It takes as input a BAM file generated by an RNAseq mapper, then analyses and quantifies all splice junctions in the file before filtering (culling) those which are unlikely to be genuine.

Proper citation: Portcullis (RRID:SCR_016442) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.

Proper citation: MAxEntScan (RRID:SCR_016707) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) Copy   

•   Source: SciCrunch Registry

https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

Proper citation: Entrez (RRID:SCR_016640) Copy   

•   Source: SciCrunch Registry

https://blast.ncbi.nlm.nih.gov/moleblast/moleblast.cgi

Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results.

Proper citation: MOLE-BLAST (RRID:SCR_016644) Copy   

•   Source: SciCrunch Registry

http://ec2-52-91-98-53.compute-1.amazonaws.com/run/

Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.

Proper citation: Clonotator (RRID:SCR_016730) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/tools/vecscreen/

Software tool to screen a nucleic acid sequence for vector contamination. Detects foreign DNAs such as vector, linker, adapter, and primer regions involved in nucleotide sequences by using blast search against vector sequence database. The main unit of this tool is vecscreen program obtainable from NCBI.

Proper citation: VecScreen (RRID:SCR_016577) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/RAMPART

Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems.

Proper citation: Rampart (RRID:SCR_016742) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Rsubread.html

Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

Proper citation: Rsubread (RRID:SCR_016945) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Biostrings.html

Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Proper citation: Biostrings (RRID:SCR_016949) Copy   

•   Source: SciCrunch Registry

http://prosightlite.northwestern.edu/

Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.

Proper citation: ProSight Lite (RRID:SCR_016908) Copy   

•   Source: SciCrunch Registry