Hi,
I have processed my data using qiime2 11.2011. I want to constract a phylogenetic as shown in attached image. could you please suggest which file and tool should i use to constract phylogenetic tree as shown in attached image.
Hi,
I have processed my data using qiime2 11.2011. I want to constract a phylogenetic as shown in attached image. could you please suggest which file and tool should i use to constract phylogenetic tree as shown in attached image.
Hi @Yogesh_Gupta,
Your attached image is not actually a phylogenetic tree. Rather it is a UPGMA clustering of samples, where the distances are unweighted UniFrac.
You can get a tree like this via qiime diversity beta-rarefaction
. The final tab of the visualization will provide a tree with bootstrap support values. We don’t really have a way to visualize the tree itself to make a pretty picture like you have, but there is a lot of tree drawing software which can help.
Thanks a lot,
here is the depth summary of sample:
> summary(depths)
Min. 1st Qu. Median Mean 3rd Qu. Max.
18396 77714 103546 112311 135904 308487
so what sampling depth should I provide and how many --p-iterations and could please suggest the tree drawing software, I tried earlier tree viewer, but it never works.
Thanks
Yogesh
Hi @ebolyen,
I am using below command please suggest if need to change the sample depth and iterations or any other input file:
qiime diversity beta-rarefaction --i-table table.qza --p-metric unweighted_unifrac --p-iterations 100 --p-sampling-depth 18000 --i-phylogeny rooted-tree.qza --output-dir UPGMA_clustering --p-clustering-method upgma --m-metadata-file metadata3.tsv --verbose
Thanks
Yogesh
Thanks for all help. waiting for your response!
Hi @ebolyen,
By using this command visualization.qzv is generated, now please suggest how can I generate the above figure from this file:
and here I used --p-iterations 100 --p-sampling-depth 18000, I am not sure if I used the correct depth figure or not?
qiime diversity beta-rarefaction --i-table table.qza --p-metric unweighted_unifrac --p-iterations 100 --p-sampling-depth 18000 --i-phylogeny rooted-tree.qza --output-dir UPGMA_clustering --p-clustering-method upgma --m-metadata-file metadata3.tsv --verbose
Thanks
Yogesh
Hi @ebolyen,
I have downloaded Newick tree file from qiime2 view and can see the tree on tree viewer. but I am getting bootstrap value in 0.23....0.50... how I can get these in the form of percent like in above figure.
I have attached the Newick tree file.
Thanks
Yogeshsample-clustering-upgma.tre (9.6 KB)
Hi @Yogesh_Gupta — those values are percentages, they are just expressed as a decimal number between zero and one. If you want to format them as percentages, you will need to consult your tree viewer’s documentation.
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