Biologists will be eager to use this biology software for research. We pick the finest free and open source biology tools for Linux.
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Tag: biology
NEST – simulator for spiking neural network models
NEST is a simulator for spiking neural network models. It focuses on the dynamics, size, and structure of neural systems.
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VCell – modeling and simulation framework
VCell is a modeling and simulation framework for computational cell biology.
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COPASI – biochemical systems simulator
COPASI is a biochemical systems simulator for building, simulating, and analyzing models of biochemical networks and their dynamics.
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napari – Python-based image viewer
napari is a Python-based image viewer aimed at researchers, scientists, and developers working with complex imaging datasets.
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CellProfiler – image analysis application for researchers
CellProfiler is an image analysis application for researchers working with microscopy data.
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11 Best Free and Open Source Web Based Genome Browsers
A Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data.
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12 Best Free and Open Source Linux Desktop Genome Browsers
There are numerous tools to browse genomes. While there’s considerable overlap in functionality, each software offers unique features or data.
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28 Best Free and Open Source Linux Bioinformatics Tools
This article identifies our favourite tools which are extremely useful for anyone interested in sequence analysis, molecular modelling, molecular dynamics, phylogenetic analysis and more.
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SeqViz – protein sequence viewer
SeqViz is a DNA, RNA, and protein sequence viewer written in the TypeScript programming language.
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NAMD – high-performance simulation of large biomolecular systems
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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VMD – molecular visualization program
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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simuPOP – general-purpose individual-based forward-time population genetics simulation environment
simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.
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MUSCLE – multiple alignment software
MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences.
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SeaView – graphical user interface for molecular phyologeny
SeaView is a multi-platform, graphical user interface for multiple sequence alignment and molecular phylogeny.
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TREE-PUZZLE – maximum likelihood analysis for nucleotide, amino acid, and two-state data
TREE-PUZZLE (previously known as PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling.
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TreeView X – phylogeny tree viewer
TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files.
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EMBOSS – software analysis package for molecular biology
EMBOSS is The European Molecular Biology Open Software Suite developed for the needs of the molecular biology (e.g. EMBnet) user community.
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GROMACS – versatile package to perform molecular dynamics
GROMACS is a molecular dynamics simulator, with building and analysis tools. It’s a versatile package to perform molecular dynamics.
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Best Free and Open Source Software – Science
Best Free and Open Source Linux Software covering physics, chemistry, biology, mathematics, data analysis, statistics, astronomy, weather, and more.
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