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http://www.greenphyl.org/

A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

Proper citation: GreenPhylDB (RRID:SCR_002834) Copy   

•   Source: SciCrunch Registry
  

https://github.com/grenaud/leeHom

Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach.

Proper citation: leeHom (RRID:SCR_002710) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/gap

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

Proper citation: NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) Copy   

•   Source: SciCrunch Registry
  

http://www.fmrib.ox.ac.uk/fsl/

Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

Proper citation: FSL (RRID:SCR_002823) Copy   

•   Source: SciCrunch Registry
  

https://github.com/PacificBiosciences/SMRT-Analysis/

Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.

Proper citation: SMRT-Analysis (RRID:SCR_002942) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/pathview.html

A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Proper citation: Pathview (RRID:SCR_002732) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/bio-rainbow/

Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Proper citation: Rainbow (RRID:SCR_002724) Copy   

•   Source: SciCrunch Registry
  

http://cpc.cbi.pku.edu.cn/

A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input.

Proper citation: Coding Potential Calculator (RRID:SCR_002764) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/rBiopaxParser.html

A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported.

Proper citation: rBiopaxParser (RRID:SCR_002744) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/sapFinder.html

An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

Proper citation: sapFinder (RRID:SCR_002685) Copy   

•   Source: SciCrunch Registry
  

http://andestools.sourceforge.net/

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

Proper citation: ANDES (RRID:SCR_002791) Copy   

•   Source: SciCrunch Registry
  

http://bioinformatics.charite.de/superpred/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits.

Proper citation: SuperPred: Drug classification and target prediction (RRID:SCR_002691) Copy   

•   Source: SciCrunch Registry
  

https://rostlab.org/owiki/index.php/PredictNLS

Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given.

Proper citation: PredictNLS (RRID:SCR_003133) Copy   

•   Source: SciCrunch Registry
  

https://github.com/arq5x/lumpy-sv/

Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.

Proper citation: LUMPY (RRID:SCR_003253) Copy   

•   Source: SciCrunch Registry
  

http://compbio.cs.sfu.ca/software-novelseq

Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

Proper citation: NovelSeq (RRID:SCR_003136) Copy   

•   Source: SciCrunch Registry
  

http://mrcanavar.sourceforge.net/

Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

Proper citation: mrCaNaVaR (RRID:SCR_003135) Copy   

•   Source: SciCrunch Registry
  

http://www.ichip.de/software/SplicingCompass.html

Software for detection of differential splicing between two different conditions using RNA-Seq data.

Proper citation: SplicingCompass (RRID:SCR_003249) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/tweeDEseq.html

Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

Proper citation: tweeDEseq (RRID:SCR_003038) Copy   

•   Source: SciCrunch Registry
  

http://abi.inf.uni-tuebingen.de/Services/MultiLoc2

An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available.

Proper citation: MultiLoc (RRID:SCR_003151) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/BRAIN.html

Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

Proper citation: BRAIN (RRID:SCR_003018) Copy   

•   Source: SciCrunch Registry