-evalue <Real>
  Expectation value (E) threshold for saving hits
  Default = '10'

-word_size <Integer, >=2>
  Word size for wordfinder algorithm

-gapopen <Integer>
  Cost to open a gap

-gapextend <Integer>
  Cost to extend a gap

-matrix <String>
  Scoring matrix name (normally BLOSUM62)

-threshold <Real, >=0>
  Minimum word score such that the word is added to the BLAST lookup
  table

-comp_based_stats <String>
  Use composition-based statistics for blastp / tblastn:
      D or d: default (equivalent to 2)
      0 or F or f: no composition-based statistics
      1: Composition-based statistics as in NAR 29:2994-3005, 2001
      2 or T or t : Composition-based score adjustment as in
      Bioinformatics 21:902-911, 2005, conditioned on sequence
      properties
      3: Composition-based score adjustment as in Bioinformatics
      21:902-911, 2005, unconditionally
  For programs other than tblastn, must either be absent or be D, F
  or 0
  Default = `2'

-num_descriptions <Integer, >=0>
  Number of database sequences to show one-line descriptions for
  Default = `500'

 -num_alignments <Integer, >=0>
  Number of database sequences to show alignments for
  Default = `250'

-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)?

-gilist <String>
  Restrict search of database to list of GI's
    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
  subject_loc

-seqidlist <String>
  Restrict search of database to list of SeqId's
    * Incompatible with:  gilist, negative_gilist, remote, subject,
  subject_loc

-negative_gilist <String>
  Restrict search of database to everything except the listed GIs
    * Incompatible with:  gilist, seqidlist, remote, subject,
      subject_loc

-entrez_query <String>
  Restrict search with the given Entrez query
    * Requires:  remote

-db_soft_mask <String>
  Filtering algorithm ID to apply to the BLAST database as soft masking
    * Incompatible with:  subject, subject_loc

-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

-evalue <Real>
  Expectation value (E) threshold for saving hits
  Default = '10'

-word_size <Integer, >=2>
  Word size for wordfinder algorithm

-gapopen <Integer>
  Cost to open a gap

-gapextend <Integer>
  Cost to extend a gap

-matrix <String>
  Scoring matrix name (normally BLOSUM62)

-threshold <Real, >=0>
  Minimum word score such that the word is added to the BLAST lookup
  table

-comp_based_stats <String>
  Use composition-based statistics for blastp / tblastn:
      D or d: default (equivalent to 2)
      0 or F or f: no composition-based statistics
      1: Composition-based statistics as in NAR 29:2994-3005, 2001
      2 or T or t : Composition-based score adjustment as in
      Bioinformatics 21:902-911, 2005, conditioned on sequence
      properties
      3: Composition-based score adjustment as in Bioinformatics
      21:902-911, 2005, unconditionally
  For programs other than tblastn, must either be absent or be D, F
  or 0
  Default = `2'

-num_descriptions <Integer, >=0>
  Number of database sequences to show one-line descriptions for
  Default = `500'

 -num_alignments <Integer, >=0>
  Number of database sequences to show alignments for
  Default = `250'

-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)?

-gilist <String>
  Restrict search of database to list of GI's
    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
  subject_loc

-seqidlist <String>
  Restrict search of database to list of SeqId's
    * Incompatible with:  gilist, negative_gilist, remote, subject,
  subject_loc

-negative_gilist <String>
  Restrict search of database to everything except the listed GIs
    * Incompatible with:  gilist, seqidlist, remote, subject,
      subject_loc

-entrez_query <String>
  Restrict search with the given Entrez query
    * Requires:  remote

-db_soft_mask <String>
  Filtering algorithm ID to apply to the BLAST database as soft masking
    * Incompatible with:  subject, subject_loc

-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