Thank you, developers, for the wonderful software package. I have a problem while trying to use my own only type strain reference database instead of the GTDB database for constructing phylogenetic trees. A similar kind of this issue was previously asked in the forum here (I would like to narrow down phlygenetic tree only based on type materials), but a solution was not suggested. Any help is well appreciated. Thank you.
Hi,
You can use the de_novo_wf to infer trees across any set of genomes and can skip the inclusion of the GTDB representative genomes using the --skip_gtdb_refs flag:
https://ecogenomics.github.io/GTDBTk/commands/de_novo_wf.html
Cheers,
Donovan
Thank you for your suggestion. It seems that I could successfully construct the phylogenetic tree using my genomes, which are type strains downloaded from the NCBI database, and my input genome.
Thank you so much!