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DessimozLab / read2tree

a tool for inferring species tree from sequencing reads
MIT License
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[Question] Marker gene for only one species #21

Closed llk578496 closed 1 year ago

llk578496 commented 1 year ago

Hello! We just tried to download the marker gene for Candida auris but seems it can't. May I know is it possible to download the market gene for only one species?

Thank you very much! Eddie

sinamajidian commented 1 year ago

Hi Eddie

Thanks for using read2tree. I'm afraid that it is not possible to to have marker genes for only on species. By definition, each orthologous group (marker genes) should include more than one gene. I would suggest to include several species/strains from the same clade of your samples (sequencing reads) in addition to one or a few outgroup species to infer a reasonable phylogeny.

Ps. Once you have the tree, you can always prune it e.g. using ete3.

Regards, Sina

llk578496 commented 1 year ago

I see. Thank a lot!