------ Trab 1 -----------

Implement dynamic program alignment using your own program and access to a WEB server. You should:

• Align 2 real proteins and 2 real genes, from the same family but from different specimens, using linear cost;
• Alignment on a remote server using SOAP or REST;
• Multiple paths;
• Align alignment;
• Interface.

You can use the [EMBOSS] package (http://emboss.sourceforge.net/) for testing and comparison.

------ Trab 2 -----------

Implementation of HMMs:

• Implement the Viterbi and Forward Algorithms for HMMs;
• Try to apply these algorithms on a bacterial genome, eg. E-Coli;
• Train the algorithms (do not need to forward);
• Compare using for training the bacteria itself, a similar bacterium and another more distant.

------ Trab 3 -----------

Implementation of phylogenetic trees:

• Implement UPGMA;
• Compare with MrBayes & Phyllip;
• Implement neighbours joining.