Does the ".full.aln" file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?
snippy-core is a tool that processes the snippy_outdir_{1..n} folders and produces the following files:


core.aln – a fasta format file that contains only the polymorphic sites (of {'A', 'C', 'T' and 'G'}) in your input set, whose length tends to decrease asymptotically as more isolates are added
core.full.aln – a fasta format file that contains all the core sites and base calls at any site where the reference has a site. The reference is not padded but the sequences mapped to it may be padded with gaps and 'N's to match the length of the reference.  The alignment length does not change as more isolates are added.


snippy{-core} was written by Torsten Seemann et al.  snp-sites was written by Andrew Page et al.   snp-sites will reduce any alignment to the core polymorphic sites (columns) and will still output a fasta.  Therefore the output of a core.aln processed through snp-sites should be the identical the input.  All fasta alignments can then be processed downstream using your tree inference package of choice (e.g., FastTree, IQ-Tree, MrBayes, BEAST ...).  If you want a distance matrix output from a fasta alignment, use something like snp-dists, also written by Torsten Seemann, or the APE package in R.  Be sure to consider how gaps and Ns are treated during this step.