Aligning Profile to Profile with MUSCLE

The Align ‣ Align profile to profile with MUSCLE context menu item allows you to align an existing profile to an active alignment. During this process, MUSCLE does not realign the profiles but inserts columns with gap characters only (‘—’ characters). For example, the alignment in the picture below could be used as a profile:

The same profile after profile-to-profile alignment:

There are two gap columns inserted into the source profile and two gap columns inserted into the added one. Therefore, the profile columns remain intact and the alignments haven’t been changed.

By aligning a profile to the active alignment, you will modify the original alignment file since it will contain two profiles after the operation is completed.