core_alignment.aln has lower and uppercase in sequences

[samuelmontgomery]

Hi,

I ran the suggested code for a core alignment (roary -e --mafft -p 8 *.gff) and the output alignment file has a combination of lower and upper case sequences
Reading the MAFFT documentation, it is related to this, where lower case is nucleotide and uppercase is amino acid sequences, but it means that only ~20% of my sequence is recognised as nucleotides for building a tree, and it isn't recognising the lower case nucleotide sequences

Any idea how to fix that?