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3-Clause BSD License: Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT: QuinlanLab, University of Utah: Bioclipse: Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) Linux, macOS, Windows [1] Eclipse Public
multiplatform (Java-based) LGPL: GenMAPP: visualize and analyze genomic data in the context of pathways Windows: Apache License: MATLAB: tool for modeling, simulating, and analyzing dynamic biological systems Windows, Linux, macOS Proprietary MEGA: free, online, open-source, phylogenetic analysis, drawing dendrograms etc. Windows/DOS-Win/Mac/Linux
OS 1 Citation ARB An integrated software environment for tree visualisation and annotation: LM [19] Archaeopteryx: Java tree viewer and editor (used to be ATV) [20] BioNumerics: Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data: W [21] Dendroscope
BioJava is an open-source software project dedicated to provide Java tools to process biological data. [1] [2] [3] BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic ...
database of protein similarities computed using FASTA: Protein model databases Swiss-model: server and repository for protein structure models Protein model databases AAindex: database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials Protein model databases BioGRID: Samuel Lunenfeld Research Institute
First Java-based systems biology modeling platform: Java: Yes: 2003 MetaMod [72] One of the first PC-based systems biology simulators: BBC Micro: No: 1986 MetaModel [73] Early PC-based systems biology simulator: Turbo Pascal 5.0: No: 1991 MIST [74] GUI based simulator: Borland Pascal 7.0: No: 1995 SCAMP [75] First application to support ...
Data Menu consists of Write Data to File, Translate/Untranslate, Select Genetic Code Table, Setup/Select Genes and Domains, Setup/Select Taxa and Groups, Quit Data Viewer. [19] Translate/Untranslate and Select Genetic Code Table is only available for nucleotide sequences.
Cytoscape was originally created at the Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002, and v1.0 was released in March 2003.