About building SILVA138 SEPP reference database - error in resolving polytomies

[chiehchangchen]

I am trying to build the SILVA 138 SEPP reference database by following the instructions in which involve removing sites that have non-gap sequences for 0.5%, to build the SILVA138.1 tree and get the masked-alignment fasta file. However, I encountered an error “ERROR: Bad base (.) at site 2347 of sequence 1” when I tried to use raxmlHPC to resolve polytomies. I am a newbie in bioinformatics and not familiar with raxmlHPC. Can anyone help me with this issue?