William,

Have you tried using .gbk files but making sure that every header field has 
some text entered (especially locus and annotation, even if the text is just a 
dot)?

Guy Plunkett has written many useful posts on this list about tweaking input 
file formats; here is one that might provide additional information:
http://sourceforge.net/p/mauve/mailman/message/31564508/

Mark


------------------------------
Mark J. Mandel, Ph.D.
Assistant Professor
Department of Microbiology-Immunology
Northwestern University Feinberg School of Medicine
320 E. Superior St., Searle 3-403
Chicago, IL 60611

m-man...@northwestern.edu
http://labs.feinberg.northwestern.edu/mandel/
(312) 503-4138 Office
(312) 503-2915 Lab
(312) 503-9594 Fax

From: William Wallace <jounieh1...@gmail.com<mailto:jounieh1...@gmail.com>>
Date: Thursday, July 2, 2015 at 10:02 PM
To: 
"mauve-users@lists.sourceforge.net<mailto:mauve-users@lists.sourceforge.net>" 
<mauve-users@lists.sourceforge.net<mailto:mauve-users@lists.sourceforge.net>>
Subject: [Mauve-users] Inquiry


 I am working on aligning bacterial strains from same species using Mauve 
software. My problem is that I cannot have annotations loaded on final image, 
although I am using ( *.faa) files from genbank where the sequences were 
accompanied with their respective annotation. Please advise.

NB: I tried to use the other file formats (.gbk), (.fna) , (.frn) and still 
unhelpful.


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