As the name might imply, MKVtools is a graphical interface for a variety of tools useful for processing video files. If you are looking to convert videos to either MP4 or AVI videos, then you should try either MP4tools or AVItools.
It will not, however, create MP4 or AVI files. This is a new and improved version of the application which will focus on what the original version was not very good at - the creation and editing of MKV files.
For users of the original MVtools (i.e., MKVtools 2), the naming convention could be a bit confusing. MKVtools is the part of the VIDEOtoolbox Suite of applications used for the creation and editing of MKV videos.
