the query is multiple different sequence

[zhaoxvwahaha]

my query is multiple different protein, if it could be as the input directly for hhblits, or must I split them into many files with each sequence in it

[milot-mirdita]

hhblits_omp and hhblits_mpi support multiple queries in the form of an ffindex database.

You can turn a while directory containing queries into a ffindex database using the ffindex_build command or all the entries of a FASTA file into a ffindex database using the ffindex_from_fasta command.