Tools   Select Another Resource Report Type

http://bmserver.sce.ntu.edu.sg/INVERTER/

Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface.

Proper citation: INVERTER (RRID:SCR_007956) Copy   

•   Source: SciCrunch Registry

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser.

Proper citation: BigWig and BigBed (RRID:SCR_007708) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/highssr/

Software that predicts microsatellites with Tandem Repeats Finder (TRF).

Proper citation: HighSSR (RRID:SCR_007949) Copy   

•   Source: SciCrunch Registry

http://genotan.sourceforge.net/

A free software tool to identify length variation of microsatellites from short sequence reads.

Proper citation: GenoTan (RRID:SCR_007935) Copy   

•   Source: SciCrunch Registry

http://enhancer.lbl.gov/

Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.

Proper citation: VISTA Enhancer Browser (RRID:SCR_007973) Copy   

•   Source: SciCrunch Registry

http://smithlab.usc.edu/histone/rseg/

Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3.

Proper citation: RSEG (RRID:SCR_007695) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/huber-srv/hilbert/

Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features.

Proper citation: HilbertVis (RRID:SCR_007862) Copy   

•   Source: SciCrunch Registry

http://brig.sourceforge.net/

A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

Proper citation: BRIG (RRID:SCR_007802) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.cicbiogune.es/AM/AnnotationModules.php

A tool for finding significant combinations of multisource annotations in gene lists.

Proper citation: Annotation-Modules (RRID:SCR_008025) Copy   

•   Source: SciCrunch Registry

http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/

Software that currently allows to process an amount of bisulfite sequencing reads obtained in one or several bisulfite sequencing experiments.

Proper citation: BiQAnalyzer HT (RRID:SCR_008045) Copy   

•   Source: SciCrunch Registry

http://erlichlab.wi.mit.edu/lobSTR/

A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: lobSTR (RRID:SCR_008030) Copy   

•   Source: SciCrunch Registry

http://www.baderlab.org/Software/ActiveDriver

A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications.

Proper citation: ActiveDriver (RRID:SCR_008104) Copy   

•   Source: SciCrunch Registry

http://drive5.com/usearch/manual/uchime_algo.html

An algorithm for detecting chimeric sequences.

Proper citation: UCHIME (RRID:SCR_008057) Copy   

•   Source: SciCrunch Registry

http://qiime.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.

Proper citation: QIIME (RRID:SCR_008249) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/RJaCGH/index.html

Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.

Proper citation: RJaCGH (RRID:SCR_008381) Copy   

•   Source: SciCrunch Registry

http://www.cerc.utexas.edu/OnlineCall/

A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.

Proper citation: OnlineCall (RRID:SCR_008263) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cipf.es/isacghtrac

Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.

Proper citation: IsaCGH (RRID:SCR_008375) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/

Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.

Proper citation: Cufflinks (RRID:SCR_014597) Copy   

•   Source: SciCrunch Registry

http://libroadrunner.org/

Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.

Proper citation: libRoadRunner (RRID:SCR_014763) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.prokka.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Prokka (RRID:SCR_014732) Copy   

•   Source: SciCrunch Registry