my question concerns extracting SNPs in Mauve from larger alignments (mine is 50 genomes, same species but quite diverse). When using alignment from a smaller subset (15 genomes) SNP extract works perfectly, but with all genomes the output file remains empty.
I let it run over night and the lack of CPU or memory doesn't seem to be the problem.
Is there a special way of dealing with larger alignments in Mauve? Are there any other ways to extract SNPs from Mauve alignment?