Tools   Select Another Resource Report Type

https://github.com/FRED-2/OptiType

Software tool for precision HLA typing from next generation sequencing data.

Proper citation: OptiType (RRID:SCR_022279) Copy   

•   Source: SciCrunch Registry

http://rrwick.github.io/Bandage/

Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies.

Proper citation: Bandage (RRID:SCR_022772) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

http://www.sailing.cs.cmu.edu/main/?page_id=511

Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.

Proper citation: SPEX2 (RRID:SCR_014923) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/orcae/

Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.

Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy   

•   Source: SciCrunch Registry

http://www.mybiosoftware.com/seaview-4-2-12-sequence-alignment-phylogenetic-tree-building.html

Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.

Proper citation: SeaView (RRID:SCR_015059) Copy   

•   Source: SciCrunch Registry

http://www.stavroX.com

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links.

Proper citation: MeroX (RRID:SCR_014956) Copy   

•   Source: SciCrunch Registry

http://busco.ezlab.org/

Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.

Proper citation: BUSCO (RRID:SCR_015008) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/giira/

Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment.

Proper citation: GIIRA (RRID:SCR_015507) Copy   

•   Source: SciCrunch Registry

http://tlife.fudan.edu.cn/ltr_finder/

Web software capable of scanning large-scale sequences for full-length LTR retrotranspsons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LTR_Finder (RRID:SCR_015247) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/hisat2/index.shtml

Graph-based alignment of next generation sequencing reads to a population of genomes.

Proper citation: HISAT2 (RRID:SCR_015530) Copy   

•   Source: SciCrunch Registry

https://github.com/johnlees/seer

Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria.

Proper citation: SEER (RRID:SCR_015499) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Proper citation: oligo (RRID:SCR_015729) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-SZ/BSVF

Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries.

Proper citation: BSVF (RRID:SCR_015727) Copy   

•   Source: SciCrunch Registry

http://www.genepattern-notebook.org/

Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code.

Proper citation: GenePattern Notebook (RRID:SCR_015699) Copy   

•   Source: SciCrunch Registry

https://github.com/larvalign/larvalign

Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping.

Proper citation: larvalign (RRID:SCR_015815) Copy   

•   Source: SciCrunch Registry

http://tissues.jensenlab.org

Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence.

Proper citation: TISSUES (RRID:SCR_015665) Copy   

•   Source: SciCrunch Registry

https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

Proper citation: Genesis (RRID:SCR_015775) Copy   

•   Source: SciCrunch Registry

https://github.com/cmayer/BaitFisher-package

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

Proper citation: Baitfisher (RRID:SCR_015985) Copy   

•   Source: SciCrunch Registry

http://avogadro.cc/

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Proper citation: Avogadro (RRID:SCR_015983) Copy   

•   Source: SciCrunch Registry