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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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Is it possible to add eukaryotic core proteins to the PhyloPhlAn database? #37

Closed charlottecc closed 4 years ago

charlottecc commented 4 years ago

Hi all,

I am new to this program and working with MAGs from skin microbiome samples. I need Malassezia yeast to be included in my database. Is there a way to add species from this genera to the precomputed database? Or do I have to create a new one with both prokaryotic and eukaryotic information?

I appreciate any help! Thanks!

fasnicar commented 4 years ago

Hi, the phylophlan database only contains marker genes for prokaryotes, so you cannot use it to study your Malassezia MAGs. To study them you should first identify a set of core genes that are also single copy from your MAGs and then use those genes as a custom database in PhyloPhlAn.

I hope this helps, Francesco