In addition to the information conveyed by the topology of the tree and the branch lengths of the tree, further information can also be written on the nodes and/or branches of the tree. The information that is available to display will depend on the tree building method and the options used. Often, support values are displayed on the tree.
Tree building methods produce the tree which best explains the information in the alignment; however, it is unlikely this tree will explain all of the variation in the alignment. Not all of the sites in the alignment will support this tree and not all of the clades in the tree will necessarily be strongly supported by the alignment. For example, with rapid speciation events, there may be insufficient information in the alignment to determine the branching pattern of a group of species, and some of the clades in the tree may have only marginally more support than alternative possible clades.
If you look at the tree you have built it is difficult to tell which clades are strongly supported and which are not. For example, does the clade containing "SIV-GSN; Greater spot-nosed monkey; AF468659" and "SIV-GSN; Greater spot-nosed monkey; AF468658" have the same support from the alignment as the clade containing "SIV-MND; Mandrill; AF328295" and "SIV-MND; Mandrill; AF367411"?
To find out how strongly the alignment supports each of the clades in the tree, we can calculate support values. In the tree building options you selected the "Bootstrap" resampling method. The bootstrap statistic for a clade in the tree is the percentage of times that clade appeared in the set of bootstrap replicate trees. This percentage ranges from 0% (the clade did not appear in any of the bootstrap trees) to 100% (the clade appeared in all of the bootstrap trees). A bootstrap replicate tree is generated by randomly sampling sites, with replacement, from the alignment, to create a new randomised alignment and then building a tree from this sampled alignment. This process is repeated for the specified number of bootstrap replicates (in your case, this was 500).
To show the bootstrap values on the tree, tick the box next to Show Branch Labels and select Consensus Support (%) from the dropdown box next to "Display".
The bootstrap value for a clade will appears to the left of the most recent common ancestral node for that clade.
Now the bootstrap values are displayed on the tree, you can see that there is strong support for the clade containing "SIV-GSN; Greater spot-nosed monkey; AF468659" and "SIV-GSN; Greater spot-nosed monkey; AF468658", but not for the clade containing "SIV-MND; Mandrill; AF328295" and "SIV-MND; Mandrill; AF367411".