===== Practical ======

=== Introduction ===

The presentation is available here:

{{:tutorials:eccb2012_t2_romainstuder.pdf.zip|}}


=== Useful tools ===

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]]

=== Part I on amino acids dataset: ===

  * [[tutorials:ECCB_T2_badasp | BADASP: Analysis of the V-type proton ATPase 116 kDa subunit a gene family ]] (Linux / MacOSX / Windows)
  * [[tutorials:ECCB_T2_tdg09 | TDG09: Analysis of the Hemagglutinin HA1 chain]] (Linux / MacOSX / Windows)
  * [[tutorials:ECCB_T2_fundi | FunDi: Analysis of the GAPDH ]] (Linux / MacOSX)
  * [[tutorials:ECCB_T2_diverge | Diverge 2: Analysis of the GAPDH ]] (Windows)


===  Part II on nucleotides dataset:===


  * [[tutorials:ECCB_T2_codeml | Codeml / PAML: Detection of positive selection in the serine/threonine-protein kinase gene family ]] (Linux / MacOSX / Windows)