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https://sourceforge.net/projects/microbiomeutil/files/

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

Proper citation: MicrobiomeUtilities (RRID:SCR_014611) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

Proper citation: FastQC (RRID:SCR_014583) Copy   

•   Source: SciCrunch Registry

http://www.gromacs.org

Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.

Proper citation: GROMACS (RRID:SCR_014565) Copy   

•   Source: SciCrunch Registry

http://www.openworm.org/

3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.

Proper citation: OpenWorm (RRID:SCR_014650) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/seqgen/

Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.

Proper citation: Seq-Gen (RRID:SCR_014934) Copy   

•   Source: SciCrunch Registry

http://abacus.gene.ucl.ac.uk/software/paml.html

Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PAML (RRID:SCR_014932) Copy   

•   Source: SciCrunch Registry

http://regulatorygenomicsgroup.org/chicago

Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CHiCAGO (RRID:SCR_014941) Copy   

•   Source: SciCrunch Registry

https://bio.tools

Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.

Proper citation: bio.tools (RRID:SCR_014695) Copy   

•   Source: SciCrunch Registry

http://www.cti.gov.br/invesalius

Software for magnetic resonance image reconstruction and computed tomography reconstruction. Its main application geared towards rapid prototyping, teaching, forensics, and medicine. Its features include the ability to import DICOM or Analyze files, to export files to the STL, OBJ, and PLY formats, volume rendering, and manual or semiautomatic image segmentation.

Proper citation: InVesalius 3 (RRID:SCR_014693) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

Proper citation: Bowtie 2 (RRID:SCR_016368) Copy   

•   Source: SciCrunch Registry

http://dgrapov.github.io/MetaMapR/

An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.

Proper citation: MetaMapR (RRID:SCR_014685) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-flexlab/SOAPnuke

Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status.

Proper citation: SOAPnuke (RRID:SCR_015025) Copy   

•   Source: SciCrunch Registry

http://www.molecularevolution.org/software/phylogenetics/jmodeltest

Software tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests, Akaike and Bayesian information criteria, and a decision theory method. It also provides estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates.

Proper citation: jModelTest (RRID:SCR_015244) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/gen3va/

Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.

Proper citation: GEN3VA (RRID:SCR_015682) Copy   

•   Source: SciCrunch Registry

http://toolkit.bcblab.com/

Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas.

Proper citation: BCBtoolkit (RRID:SCR_015519) Copy   

•   Source: SciCrunch Registry

https://cm.jefferson.edu/Off-Spotter//

Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers.

Proper citation: Off-Spotter (RRID:SCR_015739) Copy   

•   Source: SciCrunch Registry

http://www.atgc-montpellier.fr/lordec/

Software that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads.

Proper citation: LoRDEC (RRID:SCR_015814) Copy   

•   Source: SciCrunch Registry

http://ualcan.path.uab.edu/cgi-bin/ualcan-res.pl

Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses.

Proper citation: UALCAN (RRID:SCR_015827) Copy   

•   Source: SciCrunch Registry

http://app.cgu.edu.tw/circlnc/

Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data.

Proper citation: circlncRNAnet (RRID:SCR_015794) Copy   

•   Source: SciCrunch Registry

http://gigadb.org/dataset/100360

Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets.

Proper citation: VaDiR (RRID:SCR_015797) Copy   

•   Source: SciCrunch Registry