UniFrac with a design file?

I’m trying to follow the 454 SOP protocol with my data and run unifrac.weighted with a group=myfile.design. But I get back an error that the sequences it’s looking for aren’t in my group file.

I’ve tried running it a few ways.
unifrac.weighted(tree=LaSelva.final.pick.phylip.tre, group=nest.design, subsample=900, processors=2)
unifrac.weighted(tree=LaSelva.final.pick.phylip.tre, name=LaSelva.final.pick.names, group=nest.design, subsample=900, processors=2)

Nothing I’ve done has worked. Am I missing something in how I should be generating my .tre file to use with a design file? Is there another file I should be adding into the command?

I suspect your design file has the names of groups and not the names of sequences in it, right? In this case the tree would need to be made up of groups, not sequences.

Ah. I figured it was something simple I was missing. I got it working. Thanks!