ANI coding sequences + noncoding?

[TommyH-Tran]

From my understanding our ANI calculations are only for CDS, whereas others include all sequences (noncoding and coding). There are sometimes minor discrepancies in results. Is there any way get_homologues could generate ANIs using both the noncoding and coding sequences?

[brunocontrerasmoreira]

By default get_homologues.pl -A will report ANI computed from BLASTP protein alignments. As proteins are more conserved than nucleotide sequences, this should give you high identities.
Instead, get_homologues.pl -A -c 'CDS' will report ANI computed from BLASTN nucleotide CDS alignments. You can change that to -a 'tRNA,rRNA' if you wish but you won't be able to use it to intergenic regions unless they correspond to features in a GenBank file.