Editing CrocoBLAST:UserManual (section)

=3. BLAST options=
The BLAST algorithm for sequence alignment is relatively complex, and the default settings are not always optimal for identifying suitable hits in a database or retrieving only the relevant results. In case you wish to fiddle with the default BLAST settings by changing the general BLAST ''options'' or the ''options'' specific to each BLAST program. CrocoBLAST accepts almost any advanced BLAST options. Please see the NCBI web pages for a [http://www.ncbi.nlm.nih.gov/books/NBK279675/ full description of accessible BLAST options]. It is important to note that the current version of CrocoBLAST overrides the BLAST option "-num_threads", used for parallelization, and that the BLAST option "-outfmt" for output format can only be used with 3 different formats: the default pairwise format (code 0), the tabular format (code 6), and the comma-separated values format (code 10).