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https://github.com/soedinglab/hh-suite

Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments.

Proper citation: HH-suite (RRID:SCR_016133) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/DESeq2.html

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

Proper citation: DESeq2 (RRID:SCR_015687) 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://rostlab.org/node/960

Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).

Proper citation: FreeContact (RRID:SCR_016113) Copy   

•   Source: SciCrunch Registry

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://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

https://github.com/xavierdidelot/clonalorigin

Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.

Proper citation: ClonalOrigin (RRID:SCR_016061) Copy   

•   Source: SciCrunch Registry

http://www.jstacs.de/index.php/GeMoMa

Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species.

Proper citation: GeMoMa (RRID:SCR_017646) 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://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://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

https://github.com/zhanxw/MB-GAN

Software tool as deep learning simulation framework for simulating realistic microbiome data. Can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from it.

Proper citation: MB-GAN (RRID:SCR_019289) 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.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