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Day 1


Alanine Valine Phenylanine Proline Methionine Isoleucine Leucine
Hydrophobic amino acids

Asparate Glutamate Lysine Arginine
Charged amino acids

Serine Threonine Tyrosine Histidine Cysteine Asparagine Glutamine Tryptophan Polar amino acids




This is the list of free software recommended for the course.

Program Name Description Link
ClustalX Multiple sequence alignment program with user friendly interface ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
GeneDOC A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows. http://www.nrbsc.org/downloads/

GeneDoc 2.7.0 compatible with Windows 7

PAUP* (commercial) The best available phylogenetic tree-building software is PAUP*4.b10 (Phylogenetic Analysis Using Parsimony, Swofford, 2000). This program performs advanced phylogenetic analysis using almost all methods and criteria. http://paup.csit.fsu.edu/
MEGA The goal of the MEGA (Molecular Evolutionary Genetics Analysis) software project is to make useful methods of comparative sequence analysis easily accessible to the scientific community for research and education. http://www.megasoftware.net
TreeView TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs. http://taxonomy.zoology.gla.ac.uk/ rod/treeview.html
CnD3 Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. http://www.ncbi.nlm.nih.gov/Structure/ CN3D/cn3dinstall.shtml
Chime WWW browser plug-in, allowing structure manipulation within an browser page; based on RasMol, but with many additional features http://www.mdl.com/downloads/downloadable/index.jsp
Protein Explorer Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers. http://www.umass.edu/microbio/chime/regisfrm/