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Blender
From Quake Wiki
Blender is the free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation. Through user plugins, it supports older game model formats such as Quake & Hexen2's *.MDL, Quake 2's *.MD2, Quake 3's *.MD3, and Quake 4's *.MD5.
Add ons
MDL support: Khreathor's qmdl plugin for Quake/Hexen2.
MDL/MD2/MD3 suport: Paril's version of Khreathor's qmdl plugin adding Quake 2 & Quake 3 support.
MD5 support: KozGit's addon.