What are the main differences between PICRUSt and Tax4Fun approaches?

MicrobiomeAnalyst
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  1. PICRUSt predictions are based on the nearest neighbours using the topology of the phylogenetic tree and the distance to the next sequenced organism (it will link all OTUs even the distances are large), while Tax4Fun is based on nearest neighbours based on minimum rRNA sequence similarity.

  2. PICRUSt can only be used with Greengenes annotated OTUs while Tax4Fun depends upon SILVA labelled OTUs for their predictions.

In general, KO predictions are more complete with PICURSt, but better correspondence with Tax4Fun. A detailed comparison of Tax4Fun with PICRUSt can be found here