Getting exact mismatch data from multiple sequence alignment
I have partly answered this for know! For anyone interested i use kalign to align all 10 strains to a fasta format, then I use snp-sites to output a vcf file that can show each mismatch in accordance to the first strain in the fasta. New problem is that the alignment &quot;stretches&quot; the length of this first strain, because some of the other strains are a bit longer. This means that the position of variants are with reference to the longest strain of the 10 and not the strain I want. It can work for now, but any solution to this, would be helpful.