Alpha phylogenetic alt for stacked faith

qiime2 / q2-diversity

BSD 3-Clause "New" or "Revised" License

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Alpha phylogenetic alt for stacked faith #251

Closed gwarmstrong closed 5 years ago

gwarmstrong commented 5 years ago

This PR adds the necessary code to use the implementation of Faith's PD in https://github.com/biocore/unifrac . This method is recommended for large datasets.

Since it is fairly new, it is provided as an alternative: qiime diversity alpha-phylogenetic-alt

I have included some plots benchmarking the Stacked Faith implementation from UniFrac against scikit-bio, which is currently used in qiime diversity alpha-phylogenetic

time_memory_combined

ebolyen commented 5 years ago

Travis should have a working env file in a few hours.

gwarmstrong commented 5 years ago

Great, when that's the case I should be able to revert d3ac0c7 and have everything the way I need it

gwarmstrong commented 5 years ago

Tests passing!

gwarmstrong commented 5 years ago

Feedback has been addressed here!

ElDeveloper commented 5 years ago

👍 🎆 🍾