Hi Siavash,
First, the SEPP, TIPP, UPP and HIPPI suite look very interesting and I'm excited to try them out - SEPP in particular
I'm wondering if it would it be possible to add support for pplacer refpkgs rather than using RAxML_info files to set the pplacer parameters? I have pplacer refpkgs created with trees from FastTree and it would useful to able to work with these files directly.
Regards,
Joel