Sequential Analysis of the Origin of the Human Immunodeficiency
Virus  This example shows pairwise sequence alignment (PWSA).
PWSA has multiple applications in bioinformatics, such as
multiple sequence analysis and phylogenetic tree reconstruction.
We look at a PWSA that uses a global dynamic programming
algorithm to align each pair of sequences, and we then calculate
the pairwise distances using the Tajima-Nei metric. This gives
us a matrix of distances between sequences that we use for
inferring the phylogeny of HIV and SIV viruses. PWSA is a
computationally expensive task with complexity O(L*L*N*N), where
L is the average length of the sequences and N is the number of
sequences [Durbin, et al. Cambridge University Press, 1998].
For details about the computations, view the code for
pctdemo_setup_hivview the code for pctdemo_setup_hiv.   Related
examples:  Load the Example Settings and the Data  We start by
getting the example difficulty level. If you want to use a
different example difficulty level, use pa