maf

How do I show annotation on a multiple alignment?

Answer: 

Prerequisite: The multiple alignment needs to be in maf format.

To load a separate annotation onto each genome for a multiple
alignment in Genomeview:

Enable comparative annotations
First, go to "Configuration" under "File". Click the arrow in the top
right until the "Comparative track" menu appears. Check the box
labeled "Enable comparative annotations".

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