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".

Load data
Then click on "Load Data" under "File" and select your reference
genome, your reference genome annotation, and the multiple alignment
file. If the reference genome and its accompanying annotation (gff3)
files have contig names that match, then the multiple alignment (maf)
file may have contig names that either match exactly, or match in the
second part of a string separated by a '.'. For example, if the
reference genome sequence has a contig labeled as '7000000184993136',
and the first column of the reference annotation file is also
'7000000184993136', then the corresponding entries in the .maf file
can read either '7000000184993136' or
'Fuso_sp_7_1_V2.7000000184993136'.

To load the additional annotations to overlay onto the other genomes
in the multiple alignment, click on "Load Data" under "File" and
select your additional gff3 files, one for each genome in the multiple
alignment. When adding these additional annotation tracks, the first
column in the gff3 file must match the identifiers in the multiple
alignment .maf file exacty. If the identifier in the .maf file is
'Fuso_sp_3_1_36A2_V2.7000000185169500', then the first column in the
.gff3 must be edited to read 'Fuso_sp_3_1_36A2_V2.7000000185169500'.