I suppose that any gait analysis software is developed for a concrete kind of data.
If you focus on kinematics of gait, and you have access to a motion capture system (i.e. with body markers), they usually facilitate software to analyze some basic spatio-temporal features and export raw data to a further analysis (i.e. STT CLIMA: http://www.stt-systems.com/en/products/motion-capture/life-sciences/clima/software/).
On the other hand, you can also explore the related dynamics (by employing force insoles or treadmills) or the EMG muscle activity during gait. Normally, each of the acquiring systems should allow to export raw data to Matlab. I have been working on this issue for the last 5 years and I have solved all the problems in this regard.
One of the best ways of doing this could be by using an external system such as a VICON camera capture system or a lower budget equipment such as microsoft kinetic. You will need to write some software to use the later though
Please take a look at the Codamotion ODIN software: http://codamotion.com/index.php/applications/software
ODIN is used for collecting and storing the gait analysis data captured with our mocap system. However, it is a simple one-step process to get this marker data exported to matlab.