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https://www.statease.com/software/design-expert/

Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs.

Proper citation: Design-Expert (RRID:SCR_022671) Copy   

•   Source: SciCrunch Registry

https://gitlab.inria.fr/Phylophile/Treerecs

Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree.

Proper citation: Treerecs (RRID:SCR_024497) Copy   

•   Source: SciCrunch Registry

https://www.evalue-calculator.com/evalue/

Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences.

Proper citation: Evalue (RRID:SCR_024506) Copy   

•   Source: SciCrunch Registry

http://Mar2008.archive.ensembl.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website).

Proper citation: Ensembl Genome Browser (RRID:SCR_013367) Copy   

•   Source: SciCrunch Registry

https://www.webofscience.com/wos/woscc/advanced-search

Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database.

Proper citation: Web of Science (RRID:SCR_022706) Copy   

•   Source: SciCrunch Registry

http://support.illumina.com/sequencing/sequencing_software/casava.html

Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting

Proper citation: CASAVA (RRID:SCR_001802) Copy   

•   Source: SciCrunch Registry

http://www.sas.com

Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.

Proper citation: Statistical Analysis System (RRID:SCR_008567) Copy   

•   Source: SciCrunch Registry

http://www.scipy.org/

A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.

Proper citation: SciPy (RRID:SCR_008058) Copy   

•   Source: SciCrunch Registry

http://www.blender.org/

Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Because of the overwhelming success of the first open movie project, Ton Roosendaal, the Blender Foundation''s chairman, has established the Blender Institute. This now is the permanent office and studio to more efficiently organize the Blender Foundation goals, but especially to coordinate and facilitate Open Projects related to 3D movies, games or visual effects.

Proper citation: Blender (RRID:SCR_008606) Copy   

•   Source: SciCrunch Registry

http://scholar.google.com/

Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources

Proper citation: Google Scholar (RRID:SCR_008878) Copy   

•   Source: SciCrunch Registry

http://tcoffee.crg.cat/apps/tcoffee/do:regular

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

Proper citation: T-Coffee (RRID:SCR_011818) Copy   

•   Source: SciCrunch Registry

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Tool to search translated nucleotide databases using a protein query.

Proper citation: TBLASTN (RRID:SCR_011822) Copy   

•   Source: SciCrunch Registry

http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).

Proper citation: FGENESH (RRID:SCR_011928) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry