Martina Stoycheva

snp-sites -c doesn't produce recognisable alignment for IQtree

1

Hello, I am trying to generate a core genome tree for a bacterial plant pathogen local outbreak (_Ralstonia solanacearum_) using the output of IQtree with the output of **snp-sites -c**....

Question: Can this pipeline be used for bacterial methylation detectin.

1

Hello, In E.coli Dcm methyltransferases methylate the C5 position of the second cytosine in the sequences CCAGG and CCTGG. I was wondering if I could use your tool for detecting...

scripts/convert_refseq_to_prokka_gff.py produces only 1 chromosome output

4

Hello, I have a refseq gff that contains two chromosomes in it which I wanted to use in the panaroo pipeline. I tried using the script to convert it to...