I have 5 strains of listeria. I need to do Allele Calling and draw a tree (phylogenetics and spanning). for the calling, I used chewbbaca: I ran the contigs.fasta I got from spades, but the output doesn't look well.
What input chewbbaca needs? Do I need to do annotation first? And could I generate a tree with phyloviz from the output?
Thank you very much!