I am facing the problems to convert other files to .pza files to run in qiime2. I successfully converted otu.tsv to biom and then .qza file. However, to run alpha diversity, I need input the --i-phylogeny ARTIFACT (Phylogeny[Rooted] ) to run qiime diversity core-metrics-phylogenetic for alpha diversity analysis.
Could you suggest the way to convert the .tre file qza file.
I attached the .tre file for your reference,
Thank you so much,
Prior to importing into you can root your tree using:
- a phylogenetics / tree maniuplation package like
- a tree viewer / editor to manually root your tree:
Otherwise we provide an option to mid-point root your tree after importing into QIIME 2. You can find out more in our Phylogenetic Inference Tutorial.
Thank you very much for your kind reply,
I would like to know to more about whether the converted .tre into qza file (by ete or ape) can be used in the
commandl line : "qiime diversity core-metrics-phylogenetic"
qiime diversity core-metrics-phylogenetic
My original .tre file can be found fromt this link: closed_reference.tre - Google Drive. Currently, I do not know how to import them into qiime2 with the format .qza. Additionally, could you check for whether this table is rooted or unrooted?
Thank you very much,
Hi @lephuong07, you can import phylogenies by follow these instructions.
Yes, as long as the tool you are using outputs a standard newick formatted tree (all of them do as far as I know), you can import into QIIME 2. I noticed that you are using a closed-reference tree. These are typically already rooted. The skbio package is used to handle newick trees as outlined here.
You can import your unrooted tree, and apply a midpoint root follows:
qiime tools import \
--input-path closed_reference.tre \
--type 'Phylogeny[Unrooted]' \
qiime phylogeny midpoint-root \
--i-tree closed_reference.qza \
Otherwise you can simply replace
'Phylogeny[Rooted]' in the first command and move on to
Thank you so much for your precious time and and clear explanation, Mike. I am so happy. I think I can continue the qiime pipeline with your clear explanation.
Wish you have a nice day,
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