Hi,
If you mean convert an exisitng animated file like a character etc then fragmotion is a very good low cost solution to convert to .md2 and you can use the fully functioning demo version (nag screen included) to test your pipeline before spending the money $25.
http://www.fragmosoft.com/
If you mean to create an animated model from scratch then you'll want a better modelling application. My advice would be to rig the model properly with an armature which then gives you the option of creating a boned animated file in .b3d, .x .fbx etc again using fragmotion or a vertex animated .3ds or .md2 file.
Personally I model, skin, rig and animate in Blender, export as .b3d into Fragmotion and convert from there into whatever format I require. I can confirm Blender to .b3d to Fragmotion to .md2 works very well. I'm currently doing some lovely ultra low poly (200 tris) characters which work surprisingly well in Blitz3d with 100s of characters all running their own animations on the screen at once. md2 is a great format for this and would not be possible with boned .b3d characters (keep them for your main character or close up details etc).
HTH
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