USAGE
  rpsblast [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-db database_name]
    [-dbsize num_letters] [-entrez_query entrez_query] [-query input_file]
    [-out output_file] [-evalue evalue] [-qcov_hsp_perc float_value]
    [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value]
    [-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
    [-culling_limit int_value] [-best_hit_overhang float_value]
    [-best_hit_score_edge float_value] [-window_size int_value]
    [-lcase_masking] [-query_loc range] [-parse_deflines] [-outfmt format]
    [-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
    [-line_length line_length] [-html] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-remote] [-comp_based_stats compo]
    [-use_sw_tback] [-version]

DESCRIPTION
   Reverse Position Specific BLAST 2.6.0+

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -version
   Print version number;  ignore other arguments

 *** Input query options
 -query <File_In>
   Input file name
   Default = `-'
 -query_loc <String>
   Location on the query sequence in 1-based offsets (Format: start-stop)

 *** General search options
 -db <String>
   BLAST database name
 -out <File_Out>
   Output file name
   Default = `-'
 -evalue <Real>
   Expectation value (E) threshold for saving hits 
   Default = `10'
 -comp_based_stats <String>
   Use composition-based statistics:
       D or d: default (equivalent to 1 )
       0 or F or f: Simplified Composition-based statistics as in
   Bioinformatics 15:1000-1011, 1999
       1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001
   Default = `1'

 *** Formatting options
 -outfmt <String>
   alignment view options:
     0 = Pairwise,
     1 = Query-anchored showing identities,
     2 = Query-anchored no identities,
     3 = Flat query-anchored showing identities,
     4 = Flat query-anchored no identities,
     5 = BLAST XML,
     6 = Tabular,
     7 = Tabular with comment lines,
     8 = Seqalign (Text ASN.1),
     9 = Seqalign (Binary ASN.1),
    10 = Comma-separated values,
    11 = BLAST archive (ASN.1),
    12 = Seqalign (JSON),
    13 = Multiple-file BLAST JSON,
    14 = Multiple-file BLAST XML2,
    15 = Single-file BLAST JSON,
    16 = Single-file BLAST XML2,
    18 = Organism Report
   
   Options 6, 7 and 10 can be additionally configured to produce
   a custom format specified by space delimited format specifiers.
   The supported format specifiers are:
        qseqid means Query Seq-id
           qgi means Query GI
          qacc means Query accesion
       qaccver means Query accesion.version
          qlen means Query sequence length
        sseqid means Subject Seq-id
     sallseqid means All subject Seq-id(s), separated by a ';'
           sgi means Subject GI
        sallgi means All subject GIs
          sacc means Subject accession
       saccver means Subject accession.version
       sallacc means All subject accessions
          slen means Subject sequence length
        qstart means Start of alignment in query
          qend means End of alignment in query
        sstart means Start of alignment in subject
          send means End of alignment in subject
          qseq means Aligned part of query sequence
          sseq means Aligned part of subject sequence
        evalue means Expect value
      bitscore means Bit score
         score means Raw score
        length means Alignment length
        pident means Percentage of identical matches
        nident means Number of identical matches
      mismatch means Number of mismatches
      positive means Number of positive-scoring matches
       gapopen means Number of gap openings
          gaps means Total number of gaps
          ppos means Percentage of positive-scoring matches
        frames means Query and subject frames separated by a '/'
        qframe means Query frame
        sframe means Subject frame
          btop means Blast traceback operations (BTOP)
        staxid means Subject Taxonomy ID
      ssciname means Subject Scientific Name
      scomname means Subject Common Name
    sblastname means Subject Blast Name
     sskingdom means Subject Super Kingdom
       staxids means unique Subject Taxonomy ID(s), separated by a ';'
             (in numerical order)
     sscinames means unique Subject Scientific Name(s), separated by a ';'
     scomnames means unique Subject Common Name(s), separated by a ';'
    sblastnames means unique Subject Blast Name(s), separated by a ';'
             (in alphabetical order)
    sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
             (in alphabetical order) 
        stitle means Subject Title
    salltitles means All Subject Title(s), separated by a '<>'
       sstrand means Subject Strand
         qcovs means Query Coverage Per Subject
       qcovhsp means Query Coverage Per HSP
        qcovus means Query Coverage Per Unique Subject (blastn only)
   When not provided, the default value is:
   'qaccver saccver pident length mismatch gapopen qstart qend sstart send
   evalue bitscore', which is equivalent to the keyword 'std'
   Default = `0'
 -show_gis
   Show NCBI GIs in deflines?
 -num_descriptions <Integer, >=0>
   Number of database sequences to show one-line descriptions for
   Not applicable for outfmt > 4
   Default = `500'
    * Incompatible with:  max_target_seqs
 -num_alignments <Integer, >=0>
   Number of database sequences to show alignments for
   Default = `250'
    * Incompatible with:  max_target_seqs
 -line_length <Integer, >=1>
   Line length for formatting alignments
   Not applicable for outfmt > 4
   Default = `60'
 -html
   Produce HTML output?

 *** Query filtering options
 -seg <String>
   Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
   'no' to disable)
   Default = `no'
 -soft_masking <Boolean>
   Apply filtering locations as soft masks
   Default = `false'
 -lcase_masking
   Use lower case filtering in query and subject sequence(s)?

 *** Restrict search or results
 -entrez_query <String>
   Restrict search with the given Entrez query
    * Requires:  remote
 -qcov_hsp_perc <Real, 0..100>
   Percent query coverage per hsp
 -max_hsps <Integer, >=1>
   Set maximum number of HSPs per subject sequence to save for each query
 -culling_limit <Integer, >=0>
   If the query range of a hit is enveloped by that of at least this many
   higher-scoring hits, delete the hit
    * Incompatible with:  best_hit_overhang, best_hit_score_edge
 -best_hit_overhang <Real, (>0 and <0.5)>
   Best Hit algorithm overhang value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -best_hit_score_edge <Real, (>0 and <0.5)>
   Best Hit algorithm score edge value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -max_target_seqs <Integer, >=1>
   Maximum number of aligned sequences to keep 
   Not applicable for outfmt <= 4
   Default = `500'
    * Incompatible with:  num_descriptions, num_alignments

 *** Statistical options
 -dbsize <Int8>
   Effective length of the database 
 -searchsp <Int8, >=0>
   Effective length of the search space
 -sum_stats <Boolean>
   Use sum statistics

 *** Search strategy options
 -import_search_strategy <File_In>
   Search strategy to use
    * Incompatible with:  export_search_strategy
 -export_search_strategy <File_Out>
   File name to record the search strategy used
    * Incompatible with:  import_search_strategy

 *** Extension options
 -xdrop_ungap <Real>
   X-dropoff value (in bits) for ungapped extensions
 -xdrop_gap <Real>
   X-dropoff value (in bits) for preliminary gapped extensions
 -xdrop_gap_final <Real>
   X-dropoff value (in bits) for final gapped alignment
 -window_size <Integer, >=0>
   Multiple hits window size, use 0 to specify 1-hit algorithm

 *** Miscellaneous options
 -parse_deflines
   Should the query and subject defline(s) be parsed?
 -num_threads <Integer, >=0>
   Number of threads to use in RPS BLAST search:
    0 (auto = num of databases)
    1 (disable)
    max number of threads = num of databases
   Default = `1'
    * Incompatible with:  remote
 -remote
   Execute search remotely?
    * Incompatible with:  num_threads
 -use_sw_tback
   Compute locally optimal Smith-Waterman alignments?