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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   

•   Source: SciCrunch Registry
  

https://www.open-emr.org/

Open source software for electronic health records and medical practice management solution.

Proper citation: OpenEMR (RRID:SCR_024144) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://pyscanfcs.readthedocs.io/en/stable/

Software application for perpendicular line scanning fluorescence correlation spectroscopy.

Proper citation: pyscanfcs (RRID:SCR_024190) Copy   

•   Source: SciCrunch Registry
  

https://github.com/pyranges/pyranges

Software application for efficient comparison of genomic intervals in Python.

Proper citation: pyranges (RRID:SCR_024191) Copy   

•   Source: SciCrunch Registry
  

http://gmod.org/wiki/Chado

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://launchpad.net/zalign

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://soap.genomics.org.cn/

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   

•   Source: SciCrunch Registry
  

http://idash.ucsd.edu/

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   

•   Source: SciCrunch Registry
  

https://github.com/gt1/biobambam

Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

Proper citation: biobambam (RRID:SCR_003308) Copy   

•   Source: SciCrunch Registry
  

http://phenoscape.org/

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://mgc.nci.nih.gov/

NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Mammalian Gene Collection (RRID:SCR_007024) Copy   

•   Source: SciCrunch Registry
  

https://github.com/najoshi/sickle

Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read.

Proper citation: Sickle (RRID:SCR_006800) Copy   

•   Source: SciCrunch Registry