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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
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
https://github.com/jts/nanopolish
Software package for signal-level analysis of Oxford Nanopore sequencing data.
Proper citation: Nanopolish (RRID:SCR_016157) Copy
https://github.com/sorgerlab/ashlar
Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.
Proper citation: ASHLAR (RRID:SCR_016266) Copy
Software for syntax highlighting for computational biology.
Proper citation: bioSyntax (RRID:SCR_016207) 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
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
https://omictools.com/splicing-express-tool
Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems.
Proper citation: Splicing Express (RRID:SCR_016498) Copy
https://github.com/PF2-pasteur-fr/SARTools
Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.
Proper citation: SARTools (RRID:SCR_016533) Copy
http://saclab.tamu.edu/essentiality/transit/
Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions.
Proper citation: TRANSIT (RRID:SCR_016492) Copy
https://cran.r-project.org/web/packages/anocva/index.html
Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.
Proper citation: ANOCVA (RRID:SCR_016719) Copy
https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.
Proper citation: GEO2R (RRID:SCR_016569) Copy
Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.
Proper citation: CARD (RRID:SCR_016602) Copy
https://visrsoftware.github.io/
Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.
Proper citation: VisR (RRID:SCR_016658) Copy
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