How to construct a recombination free core SNP phylogenetic tree using snippy and gubbins?

[Jessie940409]

Hi， I'm new to this and I want to construct a recombination free core SNP phylogenetic tree using snippy and gubbins. I'm confused because core.aln is a core SNP alignment file and core.full.aln is a whole genome SNP alignment file, while the input of gubbins should be a whole genome alignment file. So what should I do to get a recombination free core SNP phylogenetic tree?? Can I use core.aln as the input of gubbins?

After I got core.full.aln, if I run this: %snippy-clean_full_aln core.full.aln > clean.full.aln %run_gubbins.py -p gubbins clean.full.aln %snp-sites -c gubbins.filtered_polymorphic_sites.fasta > clean.core.aln %FastTree -gtr -nt clean.core.aln > clean.core.tree

In this case, this clean.core.tree is a recombination free core SNP phylogetneic tree or a recombination free whole SNP phylogetneic tree ???

Best wishes Jessie

[liuxq000]

Hello, I have the same problem, I don't know if the end result is a core SNP phylogetneic tree. Can you help me？