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an online tool for visualizing, annotating and managing phylogenetic trees. IcyTree [ 4] Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks. Iroki [ 5] Automatic customization and visualization of phylogenetic trees. iTOL - interactive Tree Of Life [ 6]
A Java applet that was created as supplementary demonstration material for a scientific publication A Java applet that uses 3D hardware acceleration to visualize 3D files in .pdb format downloaded from a server [1] Using applet for nontrivial animation illustrating biophysical topic (randomly moving ions pass through voltage gates) [2] Using a ...
The Control Structure Diagram [ 2][ 3] (CSD) is a control flow diagram that fits into the space normally taken by indentation in source code. Its purpose is to improve the readability of source code. jGRASP produces CSDs for Java, C, C++, Objective-C, Ada, and VHDL. The editing window provides CSD-based folding and a "context hint" feature that ...
VisualVM is a tool that provides a visual interface for viewing detailed information about Java applications while they are running on a Java Virtual Machine (JVM). VisualVM organizes JVM data that is retrieved by the Java Development Kit (JDK) tools and presents the information in a way that allows data on multiple Java applications to be quickly viewed—both local applications and ...
Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment. Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx. Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments.
Prefuse is a Java -based toolkit for building interactive information visualization applications. It supports a rich set of features for data modeling, visualization and interaction. It provides optimized data structures for tables, graphs, and trees, a host of layout and visual encoding techniques, and support for animation, dynamic queries ...
Java: Free to use software to digitize geological cross-sections, and display and edit borehole logs Geoscience ANALYST [30] Free 3D visualization and communication software for integrated, multi-disciplinary geoscience and mining data and models, which also connects to Python through geoh5py, its open-source API Mira Geoscience Ltd.
Python. PyCharm – Cross-platform Python IDE with code inspections available for analyzing code on-the-fly in the editor and bulk analysis of the whole project. PyDev – Eclipse-based Python IDE with code analysis available on-the-fly in the editor or at save time. Pylint – Static code analyzer.