Maximum number of HSPs (alignments) to keep for any single query-subject pair. Ties are broken by order of sequences in the database. Not compatible with num_descriptions or num_alignments. Use with report formats that do not have separate definition line and alignment sections such as tabular (all outfmt > 4). Show alignments for this number of database sequences. Show one-line descriptions for this number of database sequences. Location on the subject sequence (Format: start-stop). Location on the query sequence (Format: start-stop) opt/ncbi/blast/bin/blastn -query query.fsa -db "nt" -out mb.out legacy_ megablast -i query.fsa -d nt -o mb.out -print_only The second mode of operation is achieved by specifying the C Toolkit BLAST command line application invocation and appending the -print_only command line option as follows: $. See example in the first section of the Quick start. The first mode of operation is achieved by specifying the C Toolkit BLAST command line application invocation and optionally providing the -path argument after the command line to convert if the installation path for the BLAST+ applications differs from the default (available by invoking the script without arguments). The legacy_ script supports two modes of operation, one in which the C Toolkit BLAST command line invocation is converted and executed on behalf of the user and another which solely displays the BLAST+ application equivalent to what was provided, without executing the command. This script produces its own documentation by invoking it without any arguments. The purpose of the legacy_ PERL script is to help users make the transition from the C Toolkit BLAST command line applications to the BLAST+ applications. Use legacy_ blastall -i query -d nr -o blast.out For example, instead of using blastall -i query -d nr -o blast.out To utilize this script, simply prefix it to the invocation of the C toolkit BLAST command line application and append the -path option pointing to the installation directory of the BLAST+ applications. The easiest way to get started using the BLAST+ command line applications is by means of the legacy_ PERL script which is bundled along with the BLAST+ applications.
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