There are a few published examples of a similar problem where the aim has been, e.g, to infer a tree from the HIV transmission events. Furthermore, there are a few experimentally generated phylogenies, where the ancestral sequences might have been sampled, also. There's a list of these publication with the data at http://phylonetworks.blogspot.fi/p/datasets.html. All of them use the standard phylogenetic methology, and they draw the conclusions from the tree, where the potentially ancestral and more recent samples are included in the tree as leaves.
It is not simple to offer very good advice here, since e.g. the rate and type of population change in addition to all sampling related sources of variation will affect the shape of the resulting phylogenetic tree. In addition, the potential recombination event will affect the tree and the conclusion you will be able to draw from it. If you know that the virus you are doing research on is often involved in recombination, it might be a good idea to check the sequences for possible recombination events first.
Typically the ancestral sequences are clustered with its decendants in the same branch of the tree, which might be more easily intrepreted from a star-shaped or “unrooted” tree. If there are very many sequences in the tree, a “fisheye” visualization might help during the interpretation. It is also quite common for the sequences to form a ladder, if you put the first sample on the bottom of the tree (or use it as an “outgroup”). But as I said, the tree could assume very different shapes depending on your population(s) structure and sampling design.
For example, Pagan and Prank software allow insertion of sequences into an alignment using a certain position on the phylogenetic tree, which is quite close to what you're aiming at, but I do not now recall whether you could insert the ancestral states to the tree, or are they always inferred by the software. This type of solutions have really just started to appear during the recent years.