I have a number of sequences and a reference genome. I used
snippy to align each individual sequence with the reference genome. I then used
snippy-core on the
*.aln files from
snippy which produced a new
*.aln file, and a
*.full.aln. It is my understanding that the new
*.aln file contains a core SNP alignment with only bases shared by all of my sequences, and that the
*.full.aln file contains the core genome alignment with all bases of each sequence aligned to the reference genome - regardless of variation between sequences. Is my understanding correct? If not where am I going wrong?
Further, the program
snp-sites uses both the new
*.full.aln file to produce a file which can be run through
FastTree to produce a phylogenetic tree. Does this just process the files to give the phylogenetic distance between each of my sequences? I don't really understand what this step achieves at all...