Hi, I need to analyze protein mutations via MAPP tool. For this tool I need have multiple alignemnt file and phylogenetic tree file. So I need to obtain homology sequences, but not so closely related ones, because closely related sequences are not significat for MAPP. How to use BLAST to find not so close related homolgies. I tried use PSI-BLAST but:
- How many iteration is needed?
- Is inclusion_ethresh param significant?