Clustalw2 has now joined the Coot dependencies - that means that we can use it for alignments locally (yay!) This replaces the need to use MUSCLE on the EBI web server - which causes cut and paste kerfuffle, and that is entirely non-winning at tutorials.

The command to activatite is:

(run-clustalw-alignment imol chain-id target-sequence-pir-file)

although I will probably add a gui for it later.

Available in 0.9.1.