Phylogenetic tree

(Yogesh Gupta) #1

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.

(Evan Bolyen) #2

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.

1 Like
(Yogesh Gupta) #3

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

(Yogesh Gupta) #4

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

(Yogesh Gupta) #5

Thanks for all help. waiting for your response!

Confused about --p-sampling depth and and --p-max-depth
(Yogesh Gupta) #6

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

(Yogesh Gupta) #7

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)

(Matthew Ryan Dillon) assigned ebolyen #8
(Nicholas Bokulich) unassigned ebolyen #9
(Nicholas Bokulich) assigned ebolyen #10
(Matthew Ryan Dillon) unassigned ebolyen #11
(Matthew Ryan Dillon) #12

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.

(system) closed #13

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