There are a number of linux programs available that contribute in some way to the creation of panoramas. However, there is currently no complete program that offers all features rolled into one.
I use a combination of autopano-sift (actually, the GUI provided by the autopanog command), hugin and enblend - here's how.
- Use autopanog to determine the control points for stitching.
- Use hugin to fine tune the image alignment and optimise the images.
- Use enblend to blend together the images to create a panorama.
There is a great guide here: Create a Panorama.