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https://github.com/broadinstitute/pilon/

Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.

Proper citation: Pilon (RRID:SCR_014731) Copy   

•   Source: SciCrunch Registry

http://www.repeatmasker.org/RepeatModeler/

Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RepeatModeler (RRID:SCR_015027) Copy   

•   Source: SciCrunch Registry

https://morpheus.gitlab.io/

Modeling and simulation environment for study of multi scale and multicellular systems. Users can construct and simulate models of gene regulation, signaling pathways, tissue patterning and morphogenesis and explore the effects of multiscale feedbacks between these processes. Morpheus can render 2D and 3D models using graphical user interface.

Proper citation: Morpheus (RRID:SCR_014975) Copy   

•   Source: SciCrunch Registry

https://github.com/eead-csic-compbio/metagenome_Pfam_score

Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets.

Proper citation: MEBS: Multigenomic Entropy-Based Score (RRID:SCR_015708) Copy   

•   Source: SciCrunch Registry

http://rnafrabase.ibch.poznan.pl/

Engine and database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation. The database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types given for the PBD-deposited RNA structures. Knowledge of the three dimensional RNA structure is crucial for all fields of biomolecular research. In contrast to the protein field, only about 1.300 experimentally derived structures of RNAs are deposited in the Protein Data Bank (PDB). To complement the results of experimental studies, new approaches based on bioinformatics and calculation are pursued in several laboratories to make tertiary RNA structure prediction possible. RNA FRABASE version 2.0 should greatly facilitate various RNA structure modelling approaches, RNA structure analysis and motif searching. If one compares the three dimensional RNA structure to a spatial puzzle, the RNA FRABASE allows to pull out a defined piece of this puzzle - the 3D RNA fragment. The architecture of the web-accessible RNA FRABASE engine and database is based on the following information path: PDB-deposited RNA structures �� RNA sequences and secondary structures described in the dot-bracket notation �� secondary structures of RNA fragments �� 3D RNA fragments. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide on the spot structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided.

Proper citation: RNA FRABASE - RNA FRAgments search engine and dataBASE (RRID:SCR_012808) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/Roary/

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

Proper citation: Roary (RRID:SCR_018172) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/qtl2/versions/0.24

Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations.

Proper citation: R/qtl2 (RRID:SCR_018181) Copy   

•   Source: SciCrunch Registry

https://ccb.jhu.edu/software/stringtie/

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

Proper citation: StringTie (RRID:SCR_016323) Copy   

•   Source: SciCrunch Registry

https://clue.io

Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines.

Proper citation: CMap (RRID:SCR_016204) Copy   

•   Source: SciCrunch Registry

https://github.com/ruanjue/smartdenovo

Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus.

Proper citation: SMARTdenovo (RRID:SCR_017622) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap

Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.

Proper citation: pheatmap (RRID:SCR_016418) Copy   

•   Source: SciCrunch Registry

https://github.com/mahmoudibrahim/JAMM

Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately.

Proper citation: JAMM (RRID:SCR_017049) Copy   

•   Source: SciCrunch Registry

http://srv00.recas.ba.infn.it/atlas/index.html

Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided.

Proper citation: REDIportal (RRID:SCR_018490) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/NetPhos/

Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package.

Proper citation: NetPhos (RRID:SCR_017975) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.uni-muenster.de/tools/nanopipe2

Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.

Proper citation: NanoPipe (RRID:SCR_016852) Copy   

•   Source: SciCrunch Registry

http://deweylab.biostat.wisc.edu/detonate/

Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.

Proper citation: DETONATE (RRID:SCR_017035) Copy   

•   Source: SciCrunch Registry

http://www.cazy.org

Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.

Proper citation: CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/ProP/

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

Proper citation: ProP Server (RRID:SCR_014936) Copy   

•   Source: SciCrunch Registry

http://www.cprofiler.org/

Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.

Proper citation: Composition Profiler (RRID:SCR_014630) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/psa/genewise/

Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.

Proper citation: GeneWise (RRID:SCR_015054) Copy   

•   Source: SciCrunch Registry