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https://github.com/nextflow-io/nextflow
Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.
Proper citation: Nextflow (RRID:SCR_024135) Copy
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/cbrueffer/tophat-recondition
Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat.
Proper citation: TopHat-Recondition (RRID:SCR_024383) 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
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://github.com/GregoryFaust/yaha
Software tool as fast and flexible long read alignment with optimal breakpoint detection.
Proper citation: yaha (RRID:SCR_024365) 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
Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs.
Proper citation: zAlign (RRID:SCR_024360) Copy
http://cran.r-project.org/web/packages/mlgt/index.html
Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.
Proper citation: mlgt (RRID:SCR_001211) Copy
Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOAP (RRID:SCR_000689) Copy
Software tool for phylogenomic inference.
Proper citation: IQ TREE (RRID:SCR_021163) Copy
Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities.
Proper citation: QIIME2 (RRID:SCR_021258) Copy
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