Construct a Distance-Based Phylogenetic Tree

1. Go to the Mobyle Web-portal
   http://mobyle.pasteur.fr/cgi-bin/MobylePortal/portal.py
2. Enter your e-mail under heading You (in the left window).
3. Compute a distance matrix from the multiple sequence alignment using method protdist (Programs -> phylogeny -> distance -> protdist). Select distance model ``Dayhoff PAM matrix'', upload the multiple sequence alignment in PHYLIP format using the ``Browse'' button and submit the job by clicking the ``Run'' button.
4. Choose clustering method neighbor from the pull-down menu and click button ``further analysis'' in the subsection ``Outfile (PhylipDistanceMatrix)'' in the result page from the previous step.
5. Click the ``Run'' button to draw the tree.
6. Choose method drawtree from the pull-down-menu and click button ``further analysis'' in the subsection ``Neighbor output tree file (Tree)'' in the result page from the previous step.
7. Click the ``Run'' button to draw the tree.
8. Inspect the graphic tree file.

Check the quality of the reconstructed tree by bootstrapping

1. Choose method quicktree (Programs -> phylogeny -> distance -> quicktree). from the menu on the right.
2. Uploade your multiple sequence alignment in PHYLIP format using the ``Browse'' button. Set the number of bootstrapping iterations to 1000 (in the ``alignment options'' section near the bottom of the page) and submit your job by clicking the ``Run'' button.
3. Choose newicktopt (tree) from the pull-down menu and click button ``further analysis''.
4. Set option show bootstrap values to ``Yes''.
5. Click the ``Run'' buttom to draw the tree.
6. Inspect the graphic tree file.
   (Note: tree branchings with bootstrap values ≥ 70 are stably corroborated by the data)