I am trying to look genome alignment for my bacteria genome with my reference genome. From literature I came to know about Mauve tool. I am not able to understand fully to handle this tools, I have some doubts regarding this tool.
Can I use CDS (fasta or Genebank full format) as input for tooll, its possible to check the alignment? Whether only contigs are used for checking genome alignment??
My bacteria, consist of Plasmid so, I get 2files. one is CDS and Plasmid, can I do do separately alignment for these two sequence or combined? And if I take gene bank format, I feel that I am making mistake in concatenated two files.. so I used to fasta files to concatenated (CDS and Plasmid).
I have used reference genome in genbank format (.gb). or whether I have to use .fna file.
I am trying to run Mauve in windows platform with 64 bits.
Can anyone guide me, to use Mauve...