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While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage. Cytoscape can visualize and analyze network graphs of any kind involving nodes and edges (e.g., social networks). A vital aspect of the software architecture of Cytoscape is the use of plugins for specialized features.
interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js [44] phylotree.js Javascript phylotree.js is a library that extends the popular data visualization framework D3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees
A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows: Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute) Genomespace: Centralized web application that provides data format transformations and facilitates connections with other bioinformatics ...
An alignment-free bioinformatics procedure to infer distance-based phylogenetic trees from genome assemblies, specifically designed to quickly infer trees from genomes belonging to the same genus: MinHash-based pairwise genome distance, Balanced Minimum Evolution (BME), ratchet-based BME tree search, Rate of Elementary Quartets: A. Criscuolo ...
free, online, open-source, phylogenetic analysis, drawing dendrograms etc. REACTOME free, online, open-source, curated pathway database encompassing many areas of human biology WikiPathways: curate biological pathways MetaboMAPS: visualize omics data on shared metabolic pathways [1]
This is a list of free and open-source software for geological data handling and interpretation. The list is split into broad categories, depending on the intended use of the software and its scope of functionality. Notice that 'free and open-source' requires that the source code is available and users are given a free software license.
The dominant signal intensities of T 2 image weighting are fluid (white), muscle (grey), and fat (white). T 2 signals are also often emphasized or suppressed depending on what the goal of the imaging is; notable examples include fat suppression, fluid attenuation, and susceptibility weighting.
Large sample Z-test The Z-test is used to compare relative synonymous and nonsynonymous substitutions within a gene sequence, with the main objective of determining positive selection. To perform the Z-test formula, an estimation of the number of synonymous substitutions per synonymous site (dS) and nonsynonymous substitutions per nonsynonymous ...