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https://code.google.com/p/highssr/
Software that predicts microsatellites with Tandem Repeats Finder (TRF).
Proper citation: HighSSR (RRID:SCR_007949) Copy
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
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
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
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
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
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
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
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
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
http://drive5.com/usearch/manual/uchime_algo.html
An algorithm for detecting chimeric sequences.
Proper citation: UCHIME (RRID:SCR_008057) Copy
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
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
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
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
http://tree.bio.ed.ac.uk/software/figtree
A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.
Proper citation: FigTree (RRID:SCR_008515) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://mothra.ornl.gov/cgi-bin/cat/cat.cgi
A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CAT (RRID:SCR_008421) Copy
http://bioinf.uni-greifswald.de/augustus/
Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.
Proper citation: Augustus (RRID:SCR_008417) Copy
http://www.broadinstitute.org/scientific-community/science/programs/cancer/ultrasome
An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.
Proper citation: Ultrasome (RRID:SCR_008465) Copy
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