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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
128 stars 33 forks source link

Location of examples folder and database files #48

Closed KatariinaParnanen closed 3 years ago

KatariinaParnanen commented 4 years ago

Hi! Installed phylophlan using conda. I am able to succesfully print the version after installation but my phylophlan directory does dot contain an examples folder. Am I supposed to clone the examples folder from github to be able to perform the tutorials?

Also, I would like to use the nucleotide version of the default databases for other purposes. Is this found somewhere in the phylophlan directories after installation or am I able to access it from somewhere else?

fasnicar commented 4 years ago

Hi, yes, the example folders are not packaged within the conda package, so you can get the files directly from the repository if you would like to test the tutorials.

About the databases, the default ones are only proteins and there are no nucleotides versions of them, but you can use the translated search (for instance diamond) to use them with both genomes and proteomes as inputs.