tb-profiler collate has not generated the tree

[pratibha-kadam]

Dear Dr. Jody,

I have run the collate command with --itol option and it resulted in all other output files except the .tree file, as shown in the example_data.
I am attaching the command and output files below:

Please let me know what needs to be !

Regards,
Pratibha Kadam

[jodyphelan]

Hi @pratibha-kadam

The tb-profiler collate function does not perform phylogenetic reconstruction, it just produces the files required to view annotation in iTOL. If you want to create a phylogeny you will need to use a different method like snippy + iqtree or parsnp