AlignerGeneralOptionContainer

File or aligned queries

Format of aligned query file.

Sequence block size in billions of letters.

Compression for output files.

File containing custom scoring matrix.

Frame shift penalty (default=disabled)

Gap extension penalty.

Gap open penalty.

Number of targets for global ranking.

Include all subject ids in DAA file

Include full subject titles in DAA file.

Number of chunks for index processing.

Iterated search with increasing sensitivity.

Short for --range-culling --top 10 -F 15.

Score matrix for protein alignment.

Maximum number of HSPs per target sequence to report for each query.

Minimum identity percentage to report an alignment.

Minimum query cover percentage to report an alignment.

Minimum subject cover percentage to report an alignment.

Minimum bit score to report alignments (overrides e-value setting).

Suppress reporting of identical self hits.

Directory for temporary files used by multiprocessing.

Input query file.

Genetic code to use to translate query.

Restrict hit culling to overlapping query ranges.

Report unaligned queries.

Filter the database by list of accessions.

Ignore accessions missing in the database.

Query strands to search.

Exhaustive alignment against all database sequences.

Exclude list of taxon ids.

Restrict search to list of taxon ids.

File for unaligned queries.

Format of unaligned query file.