Hi @gregcaporaso,
Thanks so much for your reply and the clarification! I'm working to update my analyses to use ANCOMBC but have a followup question. The QIIME 2 tutorials that included ANCOM recommended adding a pseudo count by creating a FeatureTable[Composition] artifact; however, ANCOMBC requires that "--i-table" be a FeatureTable[Frequency] artifact (the input for the FeatureTable[Composition] artifact). Do you recommend adding a pseudo count for ANCOMBC, or does ANCOMBC do this under-the-hood/ can tolerate frequencies of zero. I found one QIIME 2 forum post (link below) that suggests that a pseudo count may be added by ANCOMBC under-the-hood but any additional clarification is greatly appreciated.
Many thanks, Caroline