I want to use phymmbl on metagenomic datasets. I first performed a test of know species and of various sequence lengths of 250bp, 500bp, 10,000bp and 100,000bp. For the sequences of length 100,000bp and 10,000bp, phymmbl is taxonomically classifying them correct except for the confidence score which it gives at 0. It is working as expected for the 250bp and 500bp.
Does anyone have any insight as to why phymmbl would do this?