How do I calculate Jaccard distance between pair-wise OTUs species

Question

[mail2steff]

Dear All, I have OTU table obtained from qiime2 analysis. I would like to get the jaccard distance between pair-wise species (not between the samples). in the output, I need disatnce matrix between the OTUs

      OTU1  OTU2  OTU3  OTU4  OTU5 
OTU1   1   0.023  0.045  0.12   0.034 
OTU2   :    :       :      :      :
OTU3   :    :       :      :      :     
OTU4   :    :       :      :      :           
OTU5   :    :       :      :      :
  

[Hann]

I do analyze the bacterial community with mothur. https://mothur.org/wiki/miseq_sop/ And you could calculate the dissimilarity indices or the distance between two communities. Using different methods that are implemented in mothur pipeline

Example Jaccard: https://mothur.org/wiki/jclass/

Answer 1

[mail2steff]

I am sorry for the simple question I got it using following.

library(philentropy)

compute the Jaccard Distance with default parameters 
distance(x,  method = "jaccard")
  

[Alex Reynolds]

Euclidean and Jaccard distances are entirely different.

[mail2steff]

I forgot to change the method in the above post