The presentation is available here:

eccb2012_t2_romainstuder.pdf.zip

Jalview: http://www.jalview.org/download.html (It could be better to increase the memory allocated to java: http://www.jalview.org/jvmmemoryparams.html )

PyMOL: http://sourceforge.net/projects/pymol/ (or http://sourceforge.net/projects/pymol/files/Legacy/)

NJplot: http://pbil.univ-lyon1.fr/software/njplot.html

• BADASP: Analysis of the V-type proton ATPase 116 kDa subunit a gene family (Linux / MacOSX / Windows)
• TDG09: Analysis of the Hemagglutinin HA1 chain (Linux / MacOSX / Windows)
• FunDi: Analysis of the GAPDH (Linux / MacOSX)
• Diverge 2: Analysis of the GAPDH (Windows)

• Codeml / PAML: Detection of positive selection in the serine/threonine-protein kinase gene family (Linux / MacOSX / Windows)