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http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bio++ (RRID:SCR_016055) Copy
http://baderlab.org/Software/EnrichmentMap
Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together.
Proper citation: EnrichmentMap (RRID:SCR_016052) Copy
https://github.com/thegenemyers/DAZZ_DB
Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.
Proper citation: Dazzler (RRID:SCR_016069) Copy
Software application to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users.
Proper citation: Dawg (RRID:SCR_016068) Copy
http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.
Proper citation: Clonalframe (RRID:SCR_016060) Copy
https://dazzlerblog.wordpress.com
Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers.
Proper citation: Daligner (RRID:SCR_016066) Copy
https://github.com/ABCD-STUDY/DEAP
Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.
Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy
https://github.com/brain-life/encode
Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes.
Proper citation: Linear Fascicle Evaluation (RRID:SCR_016153) Copy
https://github.com/CAMI-challenge/AMBER
Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.
Proper citation: AMBER (RRID:SCR_016151) Copy
Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
Proper citation: NeMOarchive (RRID:SCR_016152) Copy
https://hirnetwork.org/consortium/ctar
Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is investigating methods to increase or maintain functional beta cell mass in T1D through targeted manipulation of islet plasticity or engineered protection of beta cells from immune-mediated destruction.
Proper citation: HIRN Consortium on Targeting and Regeneration (RRID:SCR_016201) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
http://abacus.gene.ucl.ac.uk/software/indelible/
Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.
Proper citation: Indelible (RRID:SCR_016163) Copy
https://github.com/sdparekh/zUMIs
Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.
Proper citation: zUMIs (RRID:SCR_016139) Copy
https://www.microsoft.com/en-gb/
Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.
Proper citation: Microsoft Excel (RRID:SCR_016137) Copy
Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.
Proper citation: Fastml (RRID:SCR_016092) Copy
https://sanger-pathogens.github.io/gubbins/
Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Gubbins (RRID:SCR_016131) Copy
http://www.medibeacon.com/preclinical/
Software used to analyze glomerular filtration rate (GFR) measurement from MediBeacon GFR monitor. It is used with the Transdermal Continuous Renal Function Monitor.
Proper citation: MediBeacon Studio Software (RRID:SCR_016252) Copy
Text-mining software that reviews methods sections of scientific articles. It provides a numerical score to represent the "reproducibility" of the article's research.
Proper citation: SciScore (RRID:SCR_016251) Copy
https://bitbucket.org/nsegata/graphlan/wiki/Home
Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GraPhlAn (RRID:SCR_016130) Copy
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