How to get mpa_vOct22_CHOCOPhlAnSGB_202212.nwk for calculate_diversity.R? I want to calculate the Unifrac distance
Hi @pangkghm
Unfortunately, as stated in the announcement of the new release, the phylogenetic tree of the SGBs present in vOct22 is not ready yet. We are currently working on it and we will announce it in the forum and other sources (like twitter) when available.
Thanks for the new release, I am looking forward to integrating it into my pipelines. Further to pangkghm’s question, I just wonder if there is a timeline on when we might expect the newick tree to be released? I’d like to move to the latest database for pipelines but would wait for newick tree to be within the chocophlan release. Thanks!
Hi @m-crown
We just finished the reconstruction of the tree today, we need to do so manual checking to see everything went smoothly, but we hope to release in the next few days. I will keep you updated
The phylogeny for oct22 is already available here: MetaPhlAn/mpa_vOct22_CHOCOPhlAnSGB_202212.nwk at master · biobakery/MetaPhlAn · GitHub
A questions about the phylogeny/taxonomy files. Is there a way to link the IDs used in the nwk file to the full taxonomies in the tsv file? Am I missing a necessary 3rd file?
mpa_vOct22_CHOCOPhlAnSGB_202212_SGB2GTDB.tsv
mpa_vOct22_CHOCOPhlAnSGB_202212.nwk
Hi @bigdoyle
The ids of the leaves in the tree correspond to the SGB ids:
E.g. 63 would correspond to SGB63
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