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http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

http://prodata.swmed.edu/promals3d/promals3d.php

Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints.

Proper citation: PROMALS3D (RRID:SCR_018161) Copy   

•   Source: SciCrunch Registry

https://github.com/r3fang/SnapTools

Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.

Proper citation: SnapTools (RRID:SCR_018097) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/covid-19

EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.

Proper citation: EMBL-EBI COVID-19 Portal (RRID:SCR_018337) Copy   

•   Source: SciCrunch Registry

https://bigd.big.ac.cn/ncov/?lang=en

Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data.

Proper citation: 2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) Copy   

•   Source: SciCrunch Registry

http://www.vmatch.de/

Software tool for efficiently solving large scale sequence matching tasks.

Proper citation: Vmatch (RRID:SCR_018968) Copy   

•   Source: SciCrunch Registry

https://www.github.com/arq5x/poretools

Software toolkit for analyzing nanopore sequence data.

Proper citation: Poretools (RRID:SCR_015879) Copy   

•   Source: SciCrunch Registry

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

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

Proper citation: Ariba (RRID:SCR_015976) Copy   

•   Source: SciCrunch Registry

http://kmer.sourceforge.net

Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.

Proper citation: Atac (RRID:SCR_015980) Copy   

•   Source: SciCrunch Registry

https://github.com/kdmurray91/axe

Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.

Proper citation: Axe (RRID:SCR_015984) Copy   

•   Source: SciCrunch Registry

https://github.com/pezmaster31/bamtools/wiki

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

Proper citation: Bamtools (RRID:SCR_015987) Copy   

•   Source: SciCrunch Registry

https://github.com/vasilislenis/G-Anchor

Software for comparing large genomes and exploiting highly conserved sequences as evolutionary-stable "anchors". The pipeline maps a newly sequenced genome (assembled in scaffolds) on a reference genome without the need of a supercomputer.

Proper citation: G-Anchor (RRID:SCR_016046) Copy   

•   Source: SciCrunch Registry

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

Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

Proper citation: Blixem (RRID:SCR_015994) Copy   

•   Source: SciCrunch Registry

http://sing.ei.uvigo.es/ALTER/

Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.

Proper citation: ALTER (RRID:SCR_015968) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/amap-align/

Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.

Proper citation: AMAP (RRID:SCR_015969) Copy   

•   Source: SciCrunch Registry

http://mbio-serv2.mbioekol.lu.se/ARAGORN/

Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Aragorn (RRID:SCR_015974) Copy   

•   Source: SciCrunch Registry

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://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