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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://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://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://gitlab.com/SimonHTausch/HiLive

Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.

Proper citation: HiLive (RRID:SCR_016134) Copy   

•   Source: SciCrunch Registry

http://fsa.sourceforge.net/

Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned.

Proper citation: FSA (RRID:SCR_016114) Copy   

•   Source: SciCrunch Registry

https://github.com/Ashod/garli

Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.

Proper citation: GARLI (RRID:SCR_016117) Copy   

•   Source: SciCrunch Registry

https://github.com/nvalimak/fsm-lite

Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data.

Proper citation: Fsm-lite (RRID:SCR_016115) 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://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

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

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

http://www.ebi.ac.uk/compneur-srv/LGICdb/

Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

Proper citation: Ligand-Gated Ion Channel Database (RRID:SCR_002418) Copy   

•   Source: SciCrunch Registry

http://www.ifti.org/ootfd/

ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers.

Proper citation: object-oriented Transcription Factors Database (RRID:SCR_002435) Copy   

•   Source: SciCrunch Registry

http://genome.imim.es/datasets/abs2005/index.html

Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

Proper citation: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters (RRID:SCR_002276) Copy   

•   Source: SciCrunch Registry