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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. Blender's website
Add-ons
Here are some addon adding support for the following formats.
.mdl : classic vertex animated format.
.md3 : A more precise mdl used in quake3.
- Parli's mdl-md2-md3 addon for Blender based on Khreathor's
- Katsbits (old)import and export scripts, tools, and utillities
.md5 : Used in doom3 & Quake Rerelease.
- MD5 Importer/Exporter for Blender 2.80 thru Blender 3.1.2
- Katsbits (old)import and export scripts, tools, and utillities
.iqm : opensource skeletal format.
Tutorials / Help
Fairweather has a YouTube channel series: Modeling for Quake that covers many of the aspects of working with Blender for Quake modeling. Modeling for Quake