Dear Biostars Community -
I generated a de-novo assembly of my viral strain. I wanted to analyze differences of my denovo result to a reference strain, so got a very useful report from Assemblytics in conjunction with using the nucmer program from MUMmer. However the output of the alignment is in the delta format. There is delta-filterprogram to manipulate the alignment. But what I really want to do is ailgn my de-novo to the reference and have the alignment in FASTA for MAF format. The size of genome is fairly modest ( < 200kb) I was thinking of using mafft. Are there any other alignment programs that might be more appropriate?