The main thing I can tell you about this tree is that you've displayed it as a cladogram, not a phylogram, so the branch lengths are meaningless (which is why they all look so similar). If you go back into MEGA and display as a phylogram then you will have branch lengths that reflect the degree of divergence of each sequence.

As for the original ancestor, that might be easier to find if you include a proper outgroup, a sequence that is similar enough to align well, but which you know is more distantly related than any of these are to each other. Then when you root with your outgroup, your next most divergent sequence may be your earliest ancestor (hopefully, but you still need to make sense of it in terms of the ages of your isolates and any other mitigating factors).

At the moment I don't think this tree tells you much at all about how the virus has evolved, but I'm not a virologist so hopefully someone with expertise in phylogenetic epidemiology can shed more light on this.

Thank you so much!!!!!!!!!!!!!!!

is my tree correct now? Can I make any comment on the branch length now?

Hello Usama,

The branch lengths on the phylogeny are directly related to the amount of change (or genetic distance) accrued along that branch. Longer branches thus express more derivation from an ancestral state.

Your tree should display statistical support values at the nodes; for a maximum likelihood these are usually bootstrap values. Some of your nodes are not resolved, and are displayed as a polytomy (> 2 branches arising from a single node), which expresses that relationships cannot be ascertained from the data / methodology you provided. It is important to focus on the meanings of the support values, and how your method is inferring the tree. Low support and polytomies are not "failures" as such, they are objective expressions of uncertainty.

As Michael says, you will need to add a sensible outgroup to identify the ancestral state. Otherwise, you could add sequences from a closely-related gene family, and perhaps use NOTUNG to investigate the most parsimonious explanation for the pattern of gene duplication that you have on your phylogeny. In my experience, figuring out the ancestral condition on a gene tree is not a trivial thing, but perhaps others will have some good ideas on this front.

Hope that is of some help.

http://www.ncbi.nlm.nih.gov/pubmed/11108472