Tools   Select Another Resource Report Type

http://www.gzip.org/

A compression utility designed to be a replacement for compress.

Proper citation: Gzip (RRID:SCR_009291) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

Proper citation: SeqSaw (RRID:SCR_009185) Copy   

•   Source: SciCrunch Registry

http://www.medinfopoli.polimi.it/GAAS/

An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAAS (RRID:SCR_008967) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/compression/DELIMINATE/

A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion.

Proper citation: DELIMINATE (RRID:SCR_008956) Copy   

•   Source: SciCrunch Registry

https://gmod.org/wiki/CMap.1

Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)

Proper citation: CMAP (RRID:SCR_009034) Copy   

•   Source: SciCrunch Registry

http://www.ics.uci.edu/~dnazip/

DNA sequence compression using a reference genome.

Proper citation: DNAzip (RRID:SCR_009032) Copy   

•   Source: SciCrunch Registry

http://cliiq.sourceforge.net/Home

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

Proper citation: CLIIQ (RRID:SCR_009972) Copy   

•   Source: SciCrunch Registry

http://kks.inf.kcl.ac.uk/MSbind.html

Software tool that calculates features of meta-stable RNA secondary structure target sites.

Proper citation: MSbind (RRID:SCR_009910) Copy   

•   Source: SciCrunch Registry

http://hood.systemsbiology.net/rnaseqr.php

A streamlined and accurate RNA-seq sequence analysis program.

Proper citation: RNASEQR (RRID:SCR_009871) Copy   

•   Source: SciCrunch Registry

http://www.ufrgs.br/RNAi/isomiRID/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 4/1/14. Software providing a framework to find isomiRNAs, templated and non-templated modifications in microRNAs.

Proper citation: isomiRID (RRID:SCR_009809) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/1

An application for discovering potential splice junctions in high throughput sequencing (HTS) data.

Proper citation: Supersplat (RRID:SCR_009826) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/seqgen/

Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.

Proper citation: Seq-Gen (RRID:SCR_014934) Copy   

•   Source: SciCrunch Registry

http://chip-atlas.org/

Database for visualizing and making use of public ChIP-seq data. ChIP-Atlas covers almost all public ChIP-seq experiments and data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA.

Proper citation: ChIP-Atlas (RRID:SCR_015511) Copy   

•   Source: SciCrunch Registry

http://www.molecularevolution.org/software/phylogenetics/jmodeltest

Software tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests, Akaike and Bayesian information criteria, and a decision theory method. It also provides estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates.

Proper citation: jModelTest (RRID:SCR_015244) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapsnp.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPsnp (RRID:SCR_010602) Copy   

•   Source: SciCrunch Registry

http://www.isical.ac.in/~bioinfo_miu/targetminer20.htm

A robust tool for microRNA target prediction with systematic identification of negative examples.

Proper citation: TargetMiner (RRID:SCR_010573) Copy   

•   Source: SciCrunch Registry

http://jr-assembler.iis.sinica.edu.tw/

An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping.

Proper citation: JR-Assembler (RRID:SCR_010681) Copy   

•   Source: SciCrunch Registry

http://cseweb.ucsd.edu/~ppevzner/software.html#EULER-short

Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads.

Proper citation: EULER-SR (RRID:SCR_010485) Copy   

•   Source: SciCrunch Registry

http://www.genome.duke.edu/labs/ohler/research/MUMMIE/mir.html

Software for a specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.

Proper citation: MicroMUMMIE (RRID:SCR_010847) Copy   

•   Source: SciCrunch Registry

http://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) Copy   

•   Source: SciCrunch Registry