Can someone please weigh in? Perhaps there has been a change in the LEfSe software? We used our data from 2 years ago, and it is giving us a different out put than it did then. Has anyone experienced this? Thank you!
This tool has been updated once - there are two versions: https://toolshed.g2.bx.psu.edu/view/george-weingart/lefse/a31c10fe09c8
I suggest reviewing the tool version, wrapper version, parameters, and input/reference datasets used with LEfSe for the prior and current runs. The release notes for the tool will explain 3rd party changes. Also review the prior steps, tool version used for those, parameters, and the like.
Take care, Jen, Galaxy team