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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/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://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
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
http://zhanglab.ccmb.med.umich.edu/EDTSurf/
Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.
Proper citation: Edtsurf (RRID:SCR_016083) Copy
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
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
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
IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.
Proper citation: IDEPI - IDentify EPItopes (RRID:SCR_016171) Copy
https://github.com/genomeannotation/GAG
Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format.
Proper citation: Genome Annotation Generator (RRID:SCR_016053) Copy
https://savannah.gnu.org/projects/datamash/
Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.
Proper citation: Datamash (RRID:SCR_016067) Copy
Software for syntax highlighting for computational biology.
Proper citation: bioSyntax (RRID:SCR_016207) Copy
Software as an open source machine learning framework for everyone. Library for high performance numerical computation. Allows deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices.
Proper citation: tensorflow (RRID:SCR_016345) Copy
https://odmltables.readthedocs.io
Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats.
Proper citation: odMLtables (RRID:SCR_016228) Copy
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
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