Hi Mauve users I’m a new user of Mauve and have problems aligning 50 bacterial genomes – a mixture of complete genomes and incomplete genomes. It works very well with the complete genomes, but the problem arrives when I want to add the incomplete genomes consisting of multiple contigs. For each incomplete genome I have downloaded a .gbff file from genbank containing all the contigs of that genome in one file. I then thought I would be able to load the file into Mauve and that Mauve would concatenate the contigs and align these incomplete genomes with the complete genomes. However, when I add the incomplete genomes in form of the .gbff file I end up with the following message: ERROR! gap character encountered at genome sequence position 346579 Input sequences must be unaligned and ungapped! Exited with error code: -1073741819. The gap character found by Mauve seems to be the new entry –the beginning of the next contig. I have looked at the .gbff file in text format and it looks as expected for a genbank file. Can anyone tell me what I do wrong?
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