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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

--subsample None? #23

Closed adityabandla closed 4 years ago

adityabandla commented 4 years ago

The wiki says that the full alignment will be used if --subsample is set to None, however, it currently says that such an option doesn't exist

fasnicar commented 4 years ago

Hi, To use the full alignment you simply don't need to specify the --subsample option and hence its value will be None and the full alignment will be used.

adityabandla commented 4 years ago

But --subsample seems to be enforced to some preset when using --accurate and --diversity high, is there a way to make it use the full alignment when using --accurate and --diversity high?

fasnicar commented 4 years ago

You're that you cannot select that option with the preset configurations present. I'll fix this shortly and report here the commit ID that fixes this when done. Many thanks, Francesco

fasnicar commented 4 years ago

Hi, this is now fixed with commit ID 30117ce0e71a176d67f0c5d21f55f6a07fa89da8 The Bioconda package will not be updated shortly, so for the moment, please get PhyloPhlAn from the repository.

Many thanks, Francesco