snp-sites -C with gubbins outputs

[djbradshaw2]

Dear snp-sites developers,

I am following the workflow suggested by the snippy GitHub (https://github.com/tseemann/snippy) to make a core SNP tree after gubbins has identified recombinant sites. I would like to use another tool besides FastTree though for phylogenetic tree creation such as IQTree which performs better with the constant sites identified per tseemann/snippy#362.

I understand I need to use snp-sites -c on the <file_name>.filtered_polymorphic_sites.fasta to get the recombinant masked core SNP alignment that can then be used in phylogenetic tree programs per the snippy GitHub, but none of the gubbins outputs seem to be usable with snp-sites -C option. Do I need to do a conversion on one of the gubbins outputs to get the invariant sites of the recombination masked alignment or do I use the snp-sites -C on the original snippy input to gubbins to get the invariant sites of the original alignment?

Thanks for your time and help.

Sincerely,

David Bradshaw