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https://github.com/nawrockie/vadr
Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families.
Proper citation: VADR (RRID:SCR_024377) Copy
http://labs.bio.unc.edu/Vision/FISH/
Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps.
Proper citation: FISH (RRID:SCR_024378) Copy
https://github.com/fccoelho/epigrass
Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.
Proper citation: Epigrass (RRID:SCR_024016) Copy
https://github.com/jnktsj/DNApi/
Software de novo adapter prediction algorithm for small RNA sequencing data.
Proper citation: DNApi (RRID:SCR_024009) Copy
http://www.danielwilson.me.uk/omegaMap.html
Software tool for detecting natural selection and recombination in DNA or RNA sequences.
Proper citation: omegaMap (RRID:SCR_024143) Copy
Open source software for electronic health records and medical practice management solution.
Proper citation: OpenEMR (RRID:SCR_024144) Copy
https://github.com/nanoporetech/tombo
Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal.
Proper citation: Tombo (RRID:SCR_024388) Copy
Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome.
Proper citation: Assemblytics (RRID:SCR_023967) Copy
https://zhanggroup.org/NW-align/
Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.
Proper citation: NW-align (RRID:SCR_024138) Copy
https://sourceforge.net/projects/microbegps/
Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates.
Proper citation: MicrobeGPS (RRID:SCR_024112) Copy
https://sourceforge.net/projects/surankco/
Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.
Proper citation: surankco (RRID:SCR_024355) Copy
https://pyscanfcs.readthedocs.io/en/stable/
Software application for perpendicular line scanning fluorescence correlation spectroscopy.
Proper citation: pyscanfcs (RRID:SCR_024190) Copy
https://github.com/pyranges/pyranges
Software application for efficient comparison of genomic intervals in Python.
Proper citation: pyranges (RRID:SCR_024191) Copy
Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.
Proper citation: Chado (RRID:SCR_024073) Copy
https://lcb.infotech.monash.edu/mustang/
Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures.
Proper citation: Mustang (RRID:SCR_024126) Copy
http://hannonlab.cshl.edu/fastx_toolkit/
Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Proper citation: FASTX-Toolkit (RRID:SCR_005534) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications.
Proper citation: iDASH (RRID:SCR_003524) Copy
Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions.
Proper citation: Phenoscape (RRID:SCR_003799) Copy
http://crab.rutgers.edu/~dslun/csdeconv/index.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.
Proper citation: CSDeconv (RRID:SCR_000016) Copy
https://github.com/amkozlov/raxml-ng
Software phylogenetic tree inference tool which uses maximum likelihood optimality criterion. Used for maximum likelihood phylogenetic inference. Offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML.
Proper citation: RAxML Next Generation (RRID:SCR_022066) Copy
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