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Software Tools
Simulation tools for teaching evolution
Web-based tools for teaching
- NCBI
- NCBI BLAST
- EBI Pairwise seq alignment
- Graphic pairwise seq alignment by dynamic programming
- Pairwise alignment applet
- EBI ClustalW
- Viterbi Applet, UMB
- WebLogo
- Online Phylogeny Construction, Marseille, France
- FirstGlance for protein structure
- Gene network central
- Gene Boy
Standalone tools for teaching and research
- MEGA4 for phylogeny
- SWISS PDB Viewer for protein structure
- Dendroscope for tree presentation
- R statistical programming and environment
- Dynetica network simulation Java
- Cytoscape for networks
Other popular computing software
- List by Paul Lewis
- Software, molecularevolution.org
- CaseIT a computer simulation tool that performs common laboratory procedures on any DNA or protein sequence.
- Online biology workbench
- SAGE an open-source equivalent of Maple
- scilab an open-source equivalent of matlab
- GGobi data visualization
- SCIRun for modeling and visualization.
- NEURON for empirically-based simulations of neurons and networks of neurons
- CN3D for protein structure.
- VMD for protein structure.
- CHIMERA for protein structure.
- Utopia visualization.
- DAVID Bioinformatics Resources at National Institute of Allergy and Infectious Diseases (NIAID), NIH.
- WEKA, machine learning and data mining.
Phylogeny
- CONSEL, tree selection
Population genetics
- http://www.sendou.soken.ac.jp/esb/innan/InnanLab/software.html
- http://przeworski.uchicago.edu/software.html
- Prichard lab
- Stephen lab
- Donelly lab
Other lists
- http://molbiol-tools.ca/molecular_biology_freeware.htm
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