Which is the best software to perform full genome alignments of strictly related species or strains and identify SNPs and InDels taking into account also the quality of the genome at every position? I’m interested in software to perform alignment of assembled genomes and not to perform alignment of short reads from next gen experiments on reference genome(s).
Hello Stefano, have you tried Mauve? (http://gel.ahabs.wisc.edu/mauve/) I use it for different purposes, but there is an option to identify SNP ans its locations. Hope this helps.
Also try, MUMMER. This is not user friendly as Mauve, but it depends on your preferences.
I am doing similar work and I have used both MAUVE and MAFFT for such alignments, but I understand MAUVE handles alignment better than MAFFT on larger, more divergent genomes.
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