If you want to enable transparency, you have to set the
transparent parameter to true in the mesh definition. In this way the alpha value passed to gl_FragColor will affect the alpha of the rendered pixels. If you are defining a material along with the mesh definition (3D model viewer mode), the alpha channel of the diffuse map will be used for transparency.
Pay attention to face ordering in the mesh file; faces with transparencies should be moved at the end of the face list in the mesh file definition, since the lib is not sorting faces before rendering. You have to ensure the correct order manually (manual editing of the OBJ or Collada mesh file).
Here is an example where the transparent faces are not pushed at the end of the list. Note how the transparency is broken while orbiting the camera.
Here is a correct example where the ordering has been fixed and a material has been defined for the mesh (3D model viewer mode).
And here is a shader example.