Tools   Select Another Resource Report Type

http://www.ncbi.nlm.nih.gov/tools/gbench/

An integrated application for viewing and analyzing sequence data.

Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy   

•   Source: SciCrunch Registry
  

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

A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.

Proper citation: ngs.plot (RRID:SCR_011795) Copy   

•   Source: SciCrunch Registry
  

http://www.cs.utah.edu/~miriah/mizbee/Overview.html

A multiscale synteny browser for exploring conservation relationships in comparative genomics data.

Proper citation: MizBee (RRID:SCR_011804) Copy   

•   Source: SciCrunch Registry
  

http://uc-echo.sourceforge.net/

Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.

Proper citation: ECHO (RRID:SCR_011851) Copy   

•   Source: SciCrunch Registry
  

http://i122server.vu-wien.ac.at/CANGS1.1/

A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.

Proper citation: CANGS (RRID:SCR_011837) Copy   

•   Source: SciCrunch Registry
  

http://code.google.com/p/condetri/

Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data.

Proper citation: ConDeTri (RRID:SCR_011838) Copy   

•   Source: SciCrunch Registry
  

http://circos.ca/

A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

Proper citation: Circos (RRID:SCR_011798) Copy   

•   Source: SciCrunch Registry
  

http://ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/

Allows detecting and removing multiple alien sequences in both ends of sequence reads.

Proper citation: AlienTrimmer (RRID:SCR_011835) Copy   

•   Source: SciCrunch Registry
  

https://github.com/najoshi/sabre

Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.

Proper citation: sabre (RRID:SCR_011843) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vsbuffalo/scythe

Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads.

Proper citation: Scythe (RRID:SCR_011844) Copy   

•   Source: SciCrunch Registry
  

http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext

A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued.

Proper citation: SeqtrimNEXT (RRID:SCR_011845) Copy   

•   Source: SciCrunch Registry
  

https://github.com/jeffdaily/parasail

Software tool as multiple sequence alignement for global, local and semi global alignments.

Proper citation: PARASAIL (RRID:SCR_021805) Copy   

•   Source: SciCrunch Registry
  

http://toppcluster.cchmc.org/

A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Proper citation: ToppCluster (RRID:SCR_001503) Copy   

•   Source: SciCrunch Registry
  

http://statalign.github.io/

Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java.

Proper citation: StatAlign (RRID:SCR_001892) Copy   

•   Source: SciCrunch Registry
  

http://www.nactem.ac.uk/facta/

Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/

Proper citation: FACTA+. (RRID:SCR_001767) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ndaniel/fusioncatcher

Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

Proper citation: FusionCatcher (RRID:SCR_000060) Copy   

•   Source: SciCrunch Registry
  

http://dissect-trans.sourceforge.net/Home

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

Proper citation: Dissect (RRID:SCR_000058) Copy   

•   Source: SciCrunch Registry
  

https://cpndb.ca/

A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.

Proper citation: cpnDB: A Chaperonin Database (RRID:SCR_002263) Copy   

•   Source: SciCrunch Registry
  

http://www.predictprotein.org/

Web application for sequence analysis and the prediction of protein structure and function. The user interface intakes protein sequences or alignments and returned multiple sequence alignments, motifs, and nuclear localization signals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Predictions for Entire Proteomes (RRID:SCR_002803) Copy   

•   Source: SciCrunch Registry
  

http://regulondb.ccg.unam.mx/

Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.

Proper citation: RegulonDB (RRID:SCR_003499) Copy   

•   Source: SciCrunch Registry