Merging .tre files post analysis

[Nur Shahir]

Hello,

I want to analyze the beta diversity using a phylogeny metric but I have over 100 samples that I ran separately.

Is there any way for me to merge the tree files from each sample? And if so, how?

-N

[justink]

Hi Nur,

If you're referring to the UPGMA trees, I'm not sure how to merge those. But OTU tables, sure: merge_otu_tables.py should point you in the right direction.

[Nur Shahir]

I know how to merge the otu tables. I've done that already.

What I need to know is whether it's possible to merge the .tre files generated for each sample, so I can perform a phylogeny metric like Unifrac.

-N

[Justin Kuczynski]

I think that's tricky. If you're doing closed-reference OTU picking, you can use the reference OTU tree. Otherwise, I'd recommend rerunning the pipeline with all 100 samples together. It's subtle to merge evolutionary trees together - cleaner often to start from the beginning.

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