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Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.
Proper citation: Seqtk (RRID:SCR_018927) Copy
Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites.
Proper citation: TFBS (RRID:SCR_015774) Copy
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
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
http://www.ball-project.org/ballview
Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.
Proper citation: BALLView (RRID:SCR_015986) Copy
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
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
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
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
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
http://sourceforge.net/projects/arden/
Software for specificity control of read alignments using an artificial reference. It estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.
Proper citation: Arden (RRID:SCR_015975) Copy
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
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
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
https://github.com/jts/nanopolish
Software package for signal-level analysis of Oxford Nanopore sequencing data.
Proper citation: Nanopolish (RRID:SCR_016157) Copy
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
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
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
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
https://web.archive.org/web/20180212152753/http://www.frantz.fi/software/gdpc.php
Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame.
Proper citation: gdpc (RRID:SCR_016119) Copy
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