Very high Faith PD values using Greengenes2 tree

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1

Hey @wasade,
I'm using your wonderful new GG2 plugin and I noticed that Faith PD values derived from the GG2 tree(2022.10.phylogeny.asv.nwk.qza) are much higher than than I'm used to. For example in a dataset of human stool 150nt V4 16S samples that I previously calculated with fragment-insertion I see Faith PD values of ~5-50, the same dataset used with GG2 is showing me values of 4000-14000. While I expected differences with the updated GG2 tree, I'm having trouble understanding how the values can be this high! Just wanted to see if this merits a closer look on my part to see if some mistakes were made or this is expected?

Thanks in advance!

2

Hi @Mehrbod_Estaki,

The lengths are scaled to the phylogenomic backbone

Best,
Daniel

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3

Good to know then that this is expected, I guess I really underestimated the complexity of the GG2 backbone, those are massive!
Thanks @wasade!

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4

Part of why we normalized branch lengths in fig1c was to express PD as a proportion of the total tree

Best,
Daniel

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