Metaphlan 3.1 phylogenetic tree

Hi, is there a phylogenetic tree available for the Metaphlan 3.1 database? I noticed there is now a Metaphlan 4 tree of SGBs now on GitHub, but we weren’t necessarily planning on switching over just yet. Thanks!

Hi @cecilia
Unfortunately, we still have not generated the phylogenetic tree for the MetaPhlAn 3.1 database. While we are planning on doing it, it will probably take a couple of months to be ready. However, the phylogenetic tree of version 3.0 contains most of the species in 3.1 and, for most of the cases, it will probably contain all the species in your profiles.

Hi, thanks for your reply!! We are indeed still using the 3.0 tree, but we’re particularly interested in a clade with several changes and additions in the 3.1 version. It would be great if you could post here when the new tree is available.

Sure, I will keep you posted

Hi @aitor.blancomiguez , I just wanted to follow up and check whether anyone has generated a tree for Metaphlan 3.1. We have a couple analyses for which we would prefer to use this version rather than redo everything with Metaphlan 4.0, but we have a substantial number of species that aren’t included in the 3.0 tree. Thanks!

We would also be interested in a phylogenic tree for Metaphlan version 3.1 database. Definitely missing 1/3 of the species of interest if we use the tree that was compatible with the 3.0 database.

Someone on Slack asked “can we have a tree for Christmas?!” lol

Thank you

Hi all, we are still working on it (it’s been running for several months already). Hopefully it would be ready by the beginning of next year

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Hi @aitor.blancomiguez

I am hoping the tree building process was successful. Is the tree for metaphlan 3.1 is now available?

Hi @neal78
Unfortunatelly, we are still working on it. The DIAMOND2 mapping is taking more time that we expected

Hi @aitor.blancomiguez , any chance this tree for Metaphlan 3.1 finished running? We have a full set of results based on Metaphlan 3.1 results and would really like to be able to include some tree-based analyses without switching to a new version. Thank you!

Hi @cecilia
The tree building process finished few days ago, we are currently manually checking it but it should be available in the following days, I will let you know when is uploaded to the repo!

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The 3.1 phylogeny is already available to download:

See also the new (currently pinned) post here:

Great - thanks so much for your efforts!