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http://sourceforge.net/projects/congrpe/

A de novo assembly algorithm for Next-Generation Sequencing technology.

Proper citation: CongrPE (RRID:SCR_013190) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/callsim/

A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.

Proper citation: CallSim (RRID:SCR_013192) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sapas/

A RNA-seq method for polyA research.

Proper citation: SAPAS (RRID:SCR_013195) Copy   

•   Source: SciCrunch Registry

http://megasun.bch.umontreal.ca/People/lartillot/www/

A Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloBayes (RRID:SCR_006402) Copy   

•   Source: SciCrunch Registry

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

Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: KOBAS (RRID:SCR_006350) Copy   

•   Source: SciCrunch Registry

http://snps.ccbr.utoronto.ca:8080/SNPdryad/

Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences.

Proper citation: SNPdryad (RRID:SCR_006414) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/QCGWAS/

Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies.

Proper citation: QCGWAS (RRID:SCR_006408) Copy   

•   Source: SciCrunch Registry

http://loschmidt.chemi.muni.cz/predictsnp/

Consensus classifier tool that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database. A stand-alone version is also available.

Proper citation: PredictSNP (RRID:SCR_006327) Copy   

•   Source: SciCrunch Registry

http://omim.org

Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources.

Proper citation: OMIM (RRID:SCR_006437) Copy   

•   Source: SciCrunch Registry

http://www.jalview.org/

A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.

Proper citation: Jalview (RRID:SCR_006459) Copy   

•   Source: SciCrunch Registry

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

Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

Proper citation: SRAdb (RRID:SCR_006524) Copy   

•   Source: SciCrunch Registry

http://bioinf.comav.upv.es/seq_crumbs/

A collection of small sequence processing utilities that are modeled after the Unix command line text processing utilities so every utility tries to perform a specific task and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utilities with Unix pipes to create complex pipelines.

Proper citation: seq crumbs (RRID:SCR_006486) Copy   

•   Source: SciCrunch Registry

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

A software package for the discovery of regulatory regions from Bis-seq data.

Proper citation: MethylSeekR (RRID:SCR_006513) Copy   

•   Source: SciCrunch Registry

http://www.LOVD.nl/

Freely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats.

Proper citation: Leiden Open Variation Database (RRID:SCR_006566) Copy   

•   Source: SciCrunch Registry

http://www.geenivaramu.ee/en/tools/gwama

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.

Proper citation: GWAMA (RRID:SCR_006624) Copy   

•   Source: SciCrunch Registry

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

Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Proper citation: casper (RRID:SCR_006613) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/splicetrap/

A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.

Proper citation: SpliceTrap (RRID:SCR_006728) Copy   

•   Source: SciCrunch Registry

https://github.com/arq5x/bedtools2

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Proper citation: BEDTools (RRID:SCR_006646) Copy   

•   Source: SciCrunch Registry

http://dictybase.org/

Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.

Proper citation: Dictyostelium discoideum genome database (RRID:SCR_006643) Copy   

•   Source: SciCrunch Registry

http://rdp.cme.msu.edu

A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow.

Proper citation: Ribosomal Database Project (RRID:SCR_006633) Copy   

•   Source: SciCrunch Registry