Hello,

Thank you for FastANI. We are using it regularly in our work. I have run into some unexpected behaviour where FastANI does not appear to give consistent results. I have a query genome Q and the reported ANI to a given reference genome R changes depending on what genomes I have in the reference list.

That is,
fastANI -q Q.fna -r R.fna -o single.tsv

Gives a different result to:
fastANI -q Q.fna --rl references.lst -o multiple.tsv

single.tsv gives: Q.fna R.fna 97.0547 1150 1325

The relevant line in multiple.tsv gives: Q.fna R.fna 97.0342 1152 1325

Why is the report ANI and number of alignment fragments different? The results change slightly as I modify the genomes in references.lst. Is this the expected behaviour? If so, it would be helpful to note this heuristic quality of FastANI in the README since these small difference do change assignments in a small number of cases when processing large genome databases which leads to confusion.