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https://github.com/HicServices/BadMedicine
Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes.
Proper citation: BadMedicine (RRID:SCR_018879) Copy
https://github.com/ylab-hi/ScanITD
Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation.
Proper citation: ScanITD (RRID:SCR_018886) Copy
https://github.com/davidebolo1993/TRiCoLOR
Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.
Proper citation: TRiCoLOR (RRID:SCR_018801) Copy
https://beikolab.cs.dal.ca/software/STAMP
Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups.
Proper citation: STAMP (RRID:SCR_018887) Copy
http://tools.dice-database.org/GOnet/)
Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.
Proper citation: GOnet (RRID:SCR_018977) Copy
http://enterobase.warwick.ac.uk/
Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.
Proper citation: EnteroBase (RRID:SCR_019019) Copy
http://dgenies.toulouse.inra.fr/
Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.
Proper citation: D-GENIES (RRID:SCR_018967) Copy
https://nanopore.usegalaxy.eu/
Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.
Proper citation: NanoGalaxy (RRID:SCR_018912) Copy
https://nrdg.github.io/fracridge
Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.
Proper citation: fracridge (RRID:SCR_019045) Copy
http://bix.ucsd.edu/repeatscout/
Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RepeatScout (RRID:SCR_014653) Copy
http://www.vicbioinformatics.com/software.prokka.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Prokka (RRID:SCR_014732) Copy
http://www.sailing.cs.cmu.edu/main/?page_id=511
Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.
Proper citation: SPEX2 (RRID:SCR_014923) Copy
https://dogma.ccbb.utexas.edu/
Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
Proper citation: DOGMA (RRID:SCR_015060) Copy
http://bioinformatics.psb.ugent.be/orcae/
Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.
Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy
http://www.mybiosoftware.com/seaview-4-2-12-sequence-alignment-phylogenetic-tree-building.html
Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.
Proper citation: SeaView (RRID:SCR_015059) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links.
Proper citation: MeroX (RRID:SCR_014956) Copy
Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.
Proper citation: BUSCO (RRID:SCR_015008) Copy
http://floresta.eead.csic.es/primers4clades
Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs.
Proper citation: primers4clades (RRID:SCR_015714) Copy
http://amp.pharm.mssm.edu/clustergrammer/
Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features.
Proper citation: clustergrammer (RRID:SCR_015681) Copy
https://bioconductor.org/packages/release/bioc/html/oligo.html
Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Proper citation: oligo (RRID:SCR_015729) Copy
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