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http://www.maizegenetics.net/tassel

Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software)

Proper citation: TASSEL (RRID:SCR_012837) Copy   

•   Source: SciCrunch Registry

http://www.gpower.hhu.de/

Data analytics software to compute statistical power analyses for many commonly used statistical tests in social and behavioral research. It can also be used to compute effect sizes and to graphically display the results of power analyses.

Proper citation: G*Power (RRID:SCR_013726) Copy   

•   Source: SciCrunch Registry

http://endnote.com

A software application which helps users build a bibliography as they write formatted papers, manuscripts and other research-rich documents. Users can search multiple databases and collect PDFs as references for papers, then organize them within EndNote. Bibliographies and citations can be compiled within Microsoft Word using built-in tools. Papers are stored within an EndNote library and can be shared with colleagues.

Proper citation: EndNote (RRID:SCR_014001) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/Prime/

Software package that uses homology modeling and fold recognition to make protein structure predictions.

Proper citation: Prime (RRID:SCR_014887) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/glmnet/index.html

Procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. The algorithm uses cyclical coordinate descent in a path-wise fashion.

Proper citation: glmnet (RRID:SCR_015505) Copy   

•   Source: SciCrunch Registry

http://www.atgc-montpellier.fr/phyml/

Web phylogeny server based on the maximum-likelihood principle.

Proper citation: PhyML (RRID:SCR_014629) Copy   

•   Source: SciCrunch Registry

http://www.statsoft.com/Products/STATISTICA/Product-Index

Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures.

Proper citation: STATISTICA (RRID:SCR_014213) Copy   

•   Source: SciCrunch Registry

http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder

A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis.

Proper citation: QmRLFS-finder (RRID:SCR_014584) Copy   

•   Source: SciCrunch Registry

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

Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Proper citation: topGO (RRID:SCR_014798) Copy   

•   Source: SciCrunch Registry

http://www.hologic.com

Commercial organization that provides services and products in global healthcare and diagnostics.

Proper citation: Hologic (RRID:SCR_015529) 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

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.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://bioinformatics.vub.ac.be/databases/databases.html

Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs

Proper citation: SABmark (RRID:SCR_011817) Copy   

•   Source: SciCrunch Registry

http://www.stata.com

Software package for statistical analysis and presentation of graphics. Statistical software for data science.

Proper citation: Stata (RRID:SCR_012763) Copy   

•   Source: SciCrunch Registry

https://github.com/ElsevierSoftwareX/SOFTX-D-15-00082

Software PCA-based toolkit for compression and analysis of molecular simulation data. Used for compression and analysis of molecular dynamics (MD) simulation data.

Proper citation: pyPCcazip (RRID:SCR_024423) Copy   

•   Source: SciCrunch Registry