Trees may be unrooted or rooted. To view the HIV tree as an unrooted tree, click one of the unrooted views under the "General" options in the panel on the right hand side of the tree view.
Unrooted trees do not tell us much about evolutionary relationships. We cannot tell which node is the ancestor and which are the descendent nodes on the tree. To establish ancestor-descendent relationships we need to identify a suitable outgroup and then root the tree on the branch separating the outgroup from the remainder of the tree (the ingroup). We can specify the root before the building the tree to produce a rooted tree, or we can specify the root after the tree is built to change an unrooted tree to a rooted tree.
When you built the tree of HIV and SIV sequences you specified an outgroup ("SIV-MON; Mona monkey; AY340701") so Geneious has produced a rooted tree. To view the tree as a rooted tree, click the rooted view under the "General" options in the panel on the right hand side of the tree view.
Rooted phylogenetic trees may be oriented horizontally, as above, or vertically. Here the time axis is implicit, running from left to right. The node at the left end of the tree is the root node, which represents the oldest point on the tree. As we move from the root node, we can identify nodes which are ancestral to their descendent clades. Working in from the tips of the tree enables us to identify close and distant relatives. The degree of relatedness of any two organisms is given by how far back on a rooted tree you must go to find their common ancestor. If, in tracing back to the common ancestor of A and B, you pass the common ancestor of A and C, then you can say that A and C are more closely related than A and B.
On a rooted tree, each node and all of its descendent nodes form a clade. This is what we would commonly refer to as a "branch" on a real tree - the physical branch and all the little branches and leaves attached to it. Because an unrooted tree lacks the time axis described above, it is inappropriate to discuss clades in that context.