General Search Options

• -task <String, Permissible values: 'tblastn' 'tblastn-fast'>
    Task to execute
    Default = 'tblastn'

• -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

• -db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
    Genetic code to use to translate database/subjects (see user manual for details)
    Default = '1' 

• -max_intron_length <Integer, >=0>
    Length of the largest intron allowed in a translated nucleotide sequence when
     linking multiple distinct alignments
    Default = '0'

• -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'

Formatting Options

• -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

Query filtering options

• -seg <String>
    Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
    or 'no' to disable)
    Default = '12 2.2 2.5'

• -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

• -gilist <String>
    Restrict search of database to list of GIs
    * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -seqidlist <String>
    Restrict search of database to list of SeqIDs
    * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_gilist <String>
    Restrict search of database to everything except the specified GIs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_seqidlist <String>
    Restrict search of database to everything except the specified SeqIDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -taxids <String>
    Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxids <String>
    Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
     subject_loc

• -taxidlist <String>
    Restrict search of database to include only the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxidlist <String>
    Restrict search of database to everything except the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxids, 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:  db_hard_mask, subject, subject_loc

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

• -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

• -subject_besthit
    Turn on best hit per subject sequence

• -max_target_seqs <Integer, >=1>
    Maximum number of aligned sequences to keep (value of 5 or more is recommended)
    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

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

• -ungapped
    Perform ungapped alignment only?

• -window_size <Integer, >=0>
    Multiple hits window size, use 0 to specify 1-hit algorithm

General Search Options

• -task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn'>
    Task to execute
    Default = 'megablast'

• -evalue <Real>
    Expectation value (E) threshold for saving hits
    Default = '10' (1000 for blastn-short)

• -word_size <Integer, >=2>
    Word size for wordfinder algorithm (length of best perfect match)

• -gapopen <Integer>
    Cost to open a gap

• -gapextend <Integer>
    Cost to extend a gap

• -penalty <Integer, <=0>
    Penalty for a nucleotide mismatch

• -reward <Integer, >=0>
    Reward for a nucleotide match

• -use_index <Boolean>
    Use MegaBLAST database index
    Default = 'false'

Formatting Options

• -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'

Query filtering options

• -dust <String>
    Filter query sequence with DUST (Format: 'yes', 'level window linker', or
     'no' to disable)
    Default = '20 64 1' ('no' for blastn-short)

• -soft_masking <Boolean>
    Apply filtering locations as soft masks
    Default = 'true'

• -lcase_masking
    Use lower case filtering in query and subject sequence(s)?

Restrict search or results

• -gilist <String>
    Restrict search of database to list of GIs
    * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -seqidlist <String>
    Restrict search of database to list of SeqIDs
    * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_gilist <String>
    Restrict search of database to everything except the specified GIs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_seqidlist <String>
    Restrict search of database to everything except the specified SeqIDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -taxids <String>
    Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxids <String>
    Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
     subject_loc

• -taxidlist <String>
    Restrict search of database to include only the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxidlist <String>
    Restrict search of database to everything except the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxids, 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:  db_hard_mask, subject, subject_loc

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

• -perc_identity <Real, 0..100>
    Percent identity

• -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

• -subject_besthit
    Turn on best hit per subject sequence

• -max_target_seqs <Integer, >=1>
    Maximum number of aligned sequences to keep (value of 5 or more is recommended)
    Default = '500'
    * Incompatible with:  num_descriptions, num_alignments

Discontiguous MegaBLAST options

• -template_type <String, `coding', `coding_and_optimal', `optimal'>
    Discontiguous MegaBLAST template type
    * Requires:  template_length

• -template_length <Integer, Permissible values: '16' '18' '21' >
    Discontiguous MegaBLAST template length
    * Requires:  template_type

Statistical options

• -dbsize <Int8>
    Effective length of the database

• -searchsp <Int8, >=0>
    Effective length of the search space

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

• -no_greedy
    Use non-greedy dynamic programming extension

• -min_raw_gapped_score <Integer>
    Minimum raw gapped score to keep an alignment in the preliminary gapped and
     traceback stages

• -ungapped
    Perform ungapped alignment only?

• -window_size <Integer, >=0>
    Multiple hits window size, use 0 to specify 1-hit algorithm

• -off_diagonal_range <Integer, >=0>
    Number of off-diagonals to search for the 2nd hit, use 0 to turn off
    Default = `0'

Miscellaneous options

• -parse_deflines <Real>
    Should the query and subject defline(s) be parsed?

Input Query Options

• -strand <String, `both', `minus', `plus'>
    Query strand(s) to search against database/subject
    Default = 'both'

• -query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
    Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/
     taxonomyhome.html/index.cgi?chapter=cgencodes for details)
    Default = '1'

General Search Options

• -task <String, Permissible values: 'blastx' 'blastx-fast'>
    Task to execute
    Default = 'blastx'

• -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

• -max_intron_length <Integer, >=0>
    Length of the largest intron allowed in a translated nucleotide sequence when
     linking multiple distinct alignments
    Default = '0'

• -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:
        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
    Default = '2'

Formatting Options

• -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

•  -sorthits <Integer, (>=0 and =<4)>
    Sorting option for hits:
     alignment view options:
       0 = Sort by evalue,
       1 = Sort by bit score,
       2 = Sort by total score,
       3 = Sort by percent identity,
       4 = Sort by query coverage
     Not applicable for outfmt > 4

•  -sorthsps <Integer, (>=0 and =<4)>
    Sorting option for hps:
       0 = Sort by hsp evalue,
       1 = Sort by hsp score,
       2 = Sort by hsp query start,
       3 = Sort by hsp percent identity,
       4 = Sort by hsp subject start
     Not applicable for outfmt != 0

Query filtering options

• -seg <String>
    Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
    or 'no' to disable)
    Default = '12 2.2 2.5'

• -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

• -gilist <String>
    Restrict search of database to list of GIs
    * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -seqidlist <String>
    Restrict search of database to list of SeqIDs
    * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_gilist <String>
    Restrict search of database to everything except the specified GIs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_seqidlist <String>
    Restrict search of database to everything except the specified SeqIDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -taxids <String>
    Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxids <String>
    Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
     subject_loc

• -taxidlist <String>
    Restrict search of database to include only the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxidlist <String>
    Restrict search of database to everything except the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
     subject_loc

•  -ipglist <String>
    Restrict search of database to list of IPGs
    * Incompatible with:  subject, subject_loc

•  -negative_ipglist <String>
    Restrict search of database to everything except the specified IPGs
    * Incompatible with:  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:  db_hard_mask, subject, subject_loc

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

• -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

• -subject_besthit
    Turn on best hit per subject sequence

• -max_target_seqs <Integer, >=1>
    Maximum number of aligned sequences to keep (value of 5 or more is recommended)
    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

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

• -ungapped
    Perform ungapped alignment only?

Miscellaneous options

• -parse_deflines <Real>
    Should the query and subject defline(s) be parsed?

• -use_sw_tback <Real>
    Compute locally optimal Smith-Waterman alignments?

Input Query Options

• -strand <String, `both', `minus', `plus'>
    Query strand(s) to search against database/subject
    Default = 'both'

• -query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
    Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/
     taxonomyhome.html/index.cgi?chapter=cgencodes for details)
    Default = '1'

General Search Options

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

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

• -max_intron_length <Integer, >=0>
    Length of the largest intron allowed in a translated nucleotide sequence when
     linking multiple distinct alignments
    Default = '0'

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

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

• -db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33>
    Genetic code to use to translate database/subjects (see user manual for details)
    Default = '1' 

Formatting Options

• -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

•  -sorthits <Integer, (>=0 and =<4)>
    Sorting option for hits:
     alignment view options:
       0 = Sort by evalue,
       1 = Sort by bit score,
       2 = Sort by total score,
       3 = Sort by percent identity,
       4 = Sort by query coverage
     Not applicable for outfmt > 4

•  -sorthsps <Integer, (>=0 and =<4)>
    Sorting option for hps:
       0 = Sort by hsp evalue,
       1 = Sort by hsp score,
       2 = Sort by hsp query start,
       3 = Sort by hsp percent identity,
       4 = Sort by hsp subject start
     Not applicable for outfmt != 0

Query filtering options

• -seg <String>
    Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
    or 'no' to disable)
    Default = '12 2.2 2.5'

• -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

• -gilist <String>
    Restrict search of database to list of GIs
    * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -seqidlist <String>
    Restrict search of database to list of SeqIDs
    * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_gilist <String>
    Restrict search of database to everything except the specified GIs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_seqidlist <String>
    Restrict search of database to everything except the specified SeqIDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -taxids <String>
    Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxids <String>
    Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
     subject_loc

• -taxidlist <String>
    Restrict search of database to include only the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxidlist <String>
    Restrict search of database to everything except the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxids, 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:  db_hard_mask, subject, subject_loc

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

• -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

• -subject_besthit
    Turn on best hit per subject sequence

• -max_target_seqs <Integer, >=1>
    Maximum number of aligned sequences to keep (value of 5 or more is recommended)
    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

• -sum_stats <Boolean>
    Use sum statistics

Extension options

• -xdrop_ungap <Real>
    X-dropoff value (in bits) for ungapped extensions

• -window_size <Integer, >=0>
    Multiple hits window size, use 0 to specify 1-hit algorithm

Miscellaneous options

• -parse_deflines <Real>
    Should the query and subject defline(s) be parsed?

General Search Options

• -task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'>
    Task to execute
    Default = 'blastp'

• -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:
        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
    Default = '2'

Formatting Options

• -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

•  -sorthits <Integer, (>=0 and =<4)>
    Sorting option for hits:
     alignment view options:
       0 = Sort by evalue,
       1 = Sort by bit score,
       2 = Sort by total score,
       3 = Sort by percent identity,
       4 = Sort by query coverage
     Not applicable for outfmt > 4

•  -sorthsps <Integer, (>=0 and =<4)>
    Sorting option for hps:
       0 = Sort by hsp evalue,
       1 = Sort by hsp score,
       2 = Sort by hsp query start,
       3 = Sort by hsp percent identity,
       4 = Sort by hsp subject start
     Not applicable for outfmt != 0

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

• -gilist <String>
    Restrict search of database to list of GIs
    * Incompatible with:  seqidlist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -seqidlist <String>
    Restrict search of database to list of SeqIDs
    * Incompatible with:  gilist, taxids, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_gilist <String>
    Restrict search of database to everything except the specified GIs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_seqidlist <String>
    Restrict search of database to everything except the specified SeqIDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -taxids <String>
    Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxids <String>
    Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
     subject_loc

• -taxidlist <String>
    Restrict search of database to include only the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
     negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
     subject_loc

• -negative_taxidlist <String>
    Restrict search of database to everything except the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
     negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
     subject_loc

•  -ipglist <String>
    Restrict search of database to list of IPGs
    * Incompatible with:  subject, subject_loc

•  -negative_ipglist <String>
    Restrict search of database to everything except the specified IPGs
    * Incompatible with:  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:  db_hard_mask, subject, subject_loc

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

• -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

• -subject_besthit
    Turn on best hit per subject sequence

• -max_target_seqs <Integer, >=1>
    Maximum number of aligned sequences to keep (value of 5 or more is recommended)
    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

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

• -ungapped
    Perform ungapped alignment only?

Miscellaneous options

• -parse_deflines <Real>
    Should the query and subject defline(s) be parsed?

• -use_sw_tback <Real>
    Compute locally optimal Smith-Waterman alignments?