Hi,
I’m currently exploring strain-level profiling to generate sample-by-strain abundance matrices, and came across MetaPhlAn2 in a benchmark paper. I noticed there’s now a version 4 of MetaPhlAn as well as a separate StrainPhlAn tool. However, after reading through some discussions on the help forum, it seems like the newer versions might not support generating strain-level abundance matrices in the way I need. For reference, I’ve looked at issues #1259 and #3675.
Could you confirm if this is correct? If so, would it be better to stick with MetaPhlAn2 for this specific purpose?
Thanks,
James