Is clean.core.tree file generated by fastTree after running gubbin and snippy, a recombination free core SNP tree file?

[tanusaroha]

After running snippy on multiple isolates, with command snippy-multi , i have run recombination detection tool as given:

%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

I wanted to know whether snp-sites mask recombination detected by gubbins in core full alignment file. Also, tree file generated by fastTree is it a recombination free core SNP phylogeny? if not, how can i get a core SNP alignment file which has SNP in recombination regions masked? i am beginner in phylogenomics and programming, if i have understood something wrong, kindly correct.

[Jessie940409]

I also realy want to know the tree file generated by fastTree is it a recombination free core SNP phylogeny or whole SNP phylogeny??

can I use core.aln as the input of gubbins ??