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. The MEGA application is included with the Case It download and is automatically opened by Case v705.

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