A torsionally flexible molecule is represented as a spherocylinder that undergoes fluctuations in either its cap radius (breathing mode) or its cylinder length (stretching mode). The free energy of the flexible spherocylinder is calculated in analogy with earlier work based on density functional and Onsager theories of the isotropic-nematic transition. In the Landau-de Gennes limit of this theory, there are three order parameters, corresponding to the molecular alignment, molecular shape and an alignment-shape coupling. The effect of flexibility on the primary order parameter is addressed as well as the effect of alignment on molecular shape.