Tools   Select Another Resource Report Type

https://www.cgl.ucsf.edu/chimera/

Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.

Proper citation: UCSF Chimera (RRID:SCR_004097) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/FLASH/

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

Proper citation: FLASH (RRID:SCR_005531) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/standard-RAxML

Software program for phylogenetic analyses of large datasets under maximum likelihood.

Proper citation: RAxML (RRID:SCR_006086) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.graphpad.com/

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

Proper citation: GraphPad Prism (RRID:SCR_002798) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/msa/clustalw2/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

Proper citation: Clustal W2 (RRID:SCR_002909) Copy   

•   Source: SciCrunch Registry

http://www-01.ibm.com/software/uk/analytics/spss/

Software package used for interactive, or batched, statistical analysis in social science, health sciences and marketing. Software platform offers advanced statistical analysis, a library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and deployment into applications.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago.

Proper citation: SPSS (RRID:SCR_002865) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

Proper citation: Haploview (RRID:SCR_003076) Copy   

•   Source: SciCrunch Registry

http://rsb.info.nih.gov/nih-image/index.html

Public image processing and analysis program for Macintosh.

Proper citation: NIH Image (RRID:SCR_003073) Copy   

•   Source: SciCrunch Registry

http://cytoscape.org

Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Proper citation: Cytoscape (RRID:SCR_003032) Copy   

•   Source: SciCrunch Registry

http://www.bioperl.org

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BioPerl (RRID:SCR_002989) Copy   

•   Source: SciCrunch Registry

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

Proper citation: RNAhybrid (RRID:SCR_003252) Copy   

•   Source: SciCrunch Registry

http://www.scripps.edu/researchservices/dna_array/pages/Data_Analysis_GCOS.htm

Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request.

Proper citation: GeneChip Operating Software (RRID:SCR_003408) Copy   

•   Source: SciCrunch Registry

http://bio3d.colorado.edu/imod

A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X

Proper citation: IMOD (RRID:SCR_003297) Copy   

•   Source: SciCrunch Registry

http://www.pymol.org/

A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.

Proper citation: PyMOL (RRID:SCR_000305) 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://www.biogazelle.com/qbaseplus

Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.

Proper citation: qBasePLUS (RRID:SCR_003370) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) 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