  We study the spindown of isolated neutron stars from initially rapid rotation
rates, driven by two factors: (i) gravitational wave emission due to r-modes
and (ii) magnetic braking. In the context of isolated neutron stars, we present
the first study including self-consistently the magnetic damping of r-modes in
the spin evolution. We track the spin evolution employing the RNS code, which
accounts for the rotating structure of neutron stars for various equations of
state. We find that, despite the strong damping due to the magnetic field,
r-modes alter the braking rate from pure magnetic braking for B<10^{13}G. For
realistic values of the saturation amplitude, the r-mode can also decrease the
time to reach the threshold central density for quark deconfinement. Within a
phenomenological model, we assess the gravitational waveform that would result
from r-mode driven spindown of a magnetized neutron star. To contrast with the
persistent signal during the spindown phase, we also present a preliminary
estimate of the transient gravitational wave signal from an explosive
quark-hadron phase transition, which can be a signal for the deconfinement of
quarks inside neutron stars.
