Slicer

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Slicers create the instructions for the machine(gcode) from a 3d model. The instructions are basically setting temperature, and a path with a rate of flow. How this is generated can in large part effect how the object will come out.

Slic3r,(web, github)

Cura (web, [https://github.com/daid/Cura github)

RepRapPro_Slicer

Kisslicer(not open source)

E3D(probably wip)

The page Useful_Software_Packages might also contain useful info.