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https://earray.chem.agilent.com/cghanalytics/index.html
A comprehensive design and analysis tool for setting up and interpreting your microarray experiments.
Proper citation: Agilent Genomic Workbench (RRID:SCR_010918) Copy
http://pages.cs.wisc.edu/~kliang/DBChIP/
Detects differential binding of transcription factors with ChIP-seq.
Proper citation: DBChIP (RRID:SCR_010872) Copy
http://cran.r-project.org/web/packages/DIME/index.html
R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
Proper citation: DIME (RRID:SCR_010874) Copy
http://www.cs.ucf.edu/~xiaoman/ChIPModule/ChIPModule.html
A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data.
Proper citation: ChIPModule (RRID:SCR_010877) Copy
http://bio-bwa.sourceforge.net/
Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
Proper citation: BWA (RRID:SCR_010910) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
Proper citation: ERNE (RRID:SCR_010912) Copy
http://fureylab.web.unc.edu/software/fseq/
A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.
Proper citation: F-Seq (RRID:SCR_010880) Copy
Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
Proper citation: HOMER (RRID:SCR_010881) Copy
Database for microarray data storage, retrieval, analysis, and visualization.
Proper citation: UNC Microarray Database (RRID:SCR_010979) Copy
http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer
An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data.
Proper citation: ABySS-Explorer (RRID:SCR_010980) Copy
http://dnptrapper.sourceforge.net/
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Proper citation: DNPTrapper (RRID:SCR_010981) Copy
http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors.
Proper citation: Hawkeye (RRID:SCR_010982) Copy
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
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
https://github.com/sanger-pathogens/Bio-Tradis
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Proper citation: Bio-tradis (RRID:SCR_015993) Copy
http://www.vicbioinformatics.com/software.barrnap.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Barrnap (RRID:SCR_015995) Copy
http://standage.github.io/AEGeAn
Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.
Proper citation: Aegean (RRID:SCR_015965) Copy
https://github.com/EvolBioInf/andi
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Proper citation: andi (RRID:SCR_015971) Copy
http://disulfind.dsi.unifi.it/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.
Proper citation: DISULFIND (RRID:SCR_016072) Copy
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