Phylip: http://evolution.genetics.washington.edu/phylip.html (for making trees)
Dendroscope: http://ab.inf.uni-tuebingen.de/software/dendroscope (for viewing large trees)
Jim's main idea is to use Phylip to generate a tree with of the HIV-1 sequences and then create a consensus for each node with a bootstrap value >80% (or some other value). Then do the same linkage analysis on those sequences.
He suggested to create the tree use concatenated columns of the variable regions (without gaps).
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