I don't do a lot of focus stacking but so far I have found Photoshop's focus stacking does a pretty good job.
Photoshop's Focus Stacking is also available in Photoshop Elements with either the Elements+ or Elements XXL plugins.
Out of curiosity I set up this quick and simple "test" to see how many sequence shots I need and the quality of the output.
I set up this test scene with the camera mounted on a tripod and at an angle of ~45deg to the scene. I measured, using a tape measure, the camera's sensor to be ~49cm from the 21cm mark on the ruler. I used a Canon 90D with a Sigma 17-70mm f/2.8-4 lens.
All shots were taken with
f/11, 1s, ISO 100, 70mm (112mm eq)
With the above data, my phone's DOF app told me the DOF is 2.85cm.
This is a single shot with focus set on the 21cm mark on the ruler.
I then took a sequence of shots starting with focus on the 10cm mark on the ruler and then moving across ~2cm at a time for each subsequent shot. There were 10 shots in total in the sequence with the last shot focussed on the 29cm mark on the ruler.
I did not move the camera or the scene for each sequence shot. I zoomed in to the max using live view and moved the next point of focus to the centre of the camera's LCD display and focussed manually. IS was turned off on the lens.
Below is the Photoshop focus stacked output of the 10 shots.
My Conclusion: Photoshop's Focus Stacking does a very good job.