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Software Tools

Simulation tools for teaching evolution

Web-based tools for teaching

  1. NCBI
  2. NCBI BLAST
  3. EBI Pairwise seq alignment
  4. Graphic pairwise seq alignment by dynamic programming
  5. Pairwise alignment applet
  6. EBI ClustalW
  7. Viterbi Applet, UMB
  8. WebLogo
  9. Online Phylogeny Construction, Marseille, France
  10. FirstGlance for protein structure
  11. Gene network central
  12. Gene Boy

Standalone tools for teaching and research

  1. MEGA4 for phylogeny
  2. SWISS PDB Viewer for protein structure
  3. Dendroscope for tree presentation
  4. R statistical programming and environment
  5. Dynetica network simulation Java
  6. Cytoscape for networks

Other popular computing software

  1. List by Paul Lewis
  2. Software, molecularevolution.org
  3. CaseIT a computer simulation tool that performs common laboratory procedures on any DNA or protein sequence.
  4. Online biology workbench
  5. SAGE an open-source equivalent of Maple
  6. scilab an open-source equivalent of matlab
  7. GGobi data visualization
  8. SCIRun for modeling and visualization.
  9. NEURON for empirically-based simulations of neurons and networks of neurons
  10. CN3D for protein structure.
  11. VMD for protein structure.
  12. CHIMERA for protein structure.
  13. Utopia visualization.
  14. DAVID Bioinformatics Resources at National Institute of Allergy and Infectious Diseases (NIAID), NIH.
  15. WEKA, machine learning and data mining.

Phylogeny

  1. CONSEL, tree selection

Population genetics

  1. http://www.sendou.soken.ac.jp/esb/innan/InnanLab/software.html
  2. http://przeworski.uchicago.edu/software.html
  3. Prichard lab
  4. Stephen lab
  5. Donelly lab

Other lists

  1. http://molbiol-tools.ca/molecular_biology_freeware.htm