.biom to shared?

Hey Pat,
I see that Mothur has a command to go from a shared file to .biom. I’d like to go the other direction. I have an OTUtable.biom from Qiime that I would like to port into Mothur to play with your co-occurence analyses.
Do you have an easy way to do this?
Eli Powell

I believe the make.shared() command can take a biom file as an input and convert it.

You want make.shared(biom=yourBiomFile). Then you just need to change the “dummy” label to the distance the biom file represents.

I’ve tried the make.shared(biom=) and indeed get a .shared file…however, it’s empty. Suggestions? I’m not a regular user of Mothur and am using the 1.25 version included with MacQiime if that helps.

Can you try it with our current version?

Hi all,

Does anyone know if this error was resolved? I am using the most recent version of mothur and my shared file is blank after conversion from the .biom format.


The make.shared command can process a biom file in our current version 1.36.1. If you are having trouble with your file, you can send it to mothur.bugs@gmail.com.