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http://last.cbrc.jp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LAST (RRID:SCR_006119) Copy   

•   Source: SciCrunch Registry

http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

http://prodata.swmed.edu/promals3d/promals3d.php

Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints.

Proper citation: PROMALS3D (RRID:SCR_018161) Copy   

•   Source: SciCrunch Registry

https://github.com/r3fang/SnapTools

Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.

Proper citation: SnapTools (RRID:SCR_018097) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/covid-19

EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.

Proper citation: EMBL-EBI COVID-19 Portal (RRID:SCR_018337) Copy   

•   Source: SciCrunch Registry

https://bigd.big.ac.cn/ncov/?lang=en

Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data.

Proper citation: 2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) Copy   

•   Source: SciCrunch Registry

http://www.vmatch.de/

Software tool for efficiently solving large scale sequence matching tasks.

Proper citation: Vmatch (RRID:SCR_018968) 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://ccb.jhu.edu/software/stringtie/

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

Proper citation: StringTie (RRID:SCR_016323) Copy   

•   Source: SciCrunch Registry

https://integrativeomics.shinyapps.io/pseudofun_app/

Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families.

Proper citation: PseudoFuN (RRID:SCR_017095) Copy   

•   Source: SciCrunch Registry

https://github.com/HingeAssembler/HINGE

Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution.

Proper citation: Hinge (RRID:SCR_016135) 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/brentp/duphold

Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data.

Proper citation: duphold (RRID:SCR_016938) 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

http://www.uimcimes.es/contenidos/golink?p=1

Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.

Proper citation: QModeling (RRID:SCR_016358) Copy   

•   Source: SciCrunch Registry

https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

Software package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers.

Proper citation: OGDraw (RRID:SCR_017337) 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

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

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://hihg.med.miami.edu/software-download/seqem-version-1.0

Online tool for utilizing a genotype calling algorithm for next-generation sequence data.

Proper citation: SeqEM (RRID:SCR_002021) Copy   

•   Source: SciCrunch Registry