To find the troughs, invert the ‘y’ values and use findpeaks:
Example:
x = linspace(0,250,250); % Create Data
y = 0.25*sin(0.25*pi*x) .* exp(-(x-125).^2./1000) + exp(-(x-125).^2./1000);
[pks,plocs] = findpeaks(y); % Find peaks
[trs,tlocs] = findpeaks(0.1+max(y) - y); % Find troughs
figure(1)
plot(x, y)
hold on
plot(x(plocs), y(plocs), '^r', 'MarkerFaceColor','r') % Plot peaks
plot(x(tlocs), y(tlocs), 'vg', 'MarkerFaceColor','g') % Plot troughs
hold off
grid
produces:
