The video linked below explains how to use MEGA bioinformatics software to align sequences and build trees, using one of the HIV cases as an example. Ignore comments in the video tutorial about having to download MEGA separately, as MEGA is now included with the Case It download and is already installed in the Case It folder.

Note: There is a separate bioinformatics tutorial (in PDF format) that includes a section on MEGA, along with other methods for aligning sequences and building trees. The video tutorial linked below only covers MEGA, but goes into considerably more detail, including a section on how to interpret trees. The advantage of using MEGA is that trees can be built quickly via a single command from Case It.

Video tutorial on using MEGA software to align sequences and build trees