查遍网络也没发现有对blastp参数详解的资料，blastn、blastall等资料倒是不少，所以我决定自己动手，把所有的参数解释一遍。

以下是blastp的整体用法概述：
wang@wang-ThinkStation:~/mydata/Accumulibacter/blastp-pro$ blastp -help
USAGE
  blastp [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-evalue evalue] [-word_size int_value]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-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]
    [-matrix matrix_name] [-threshold float_value] [-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] [-ungapped] [-remote] [-comp_based_stats compo]
    [-use_sw_tback] [-version]

DESCRIPTION
   Protein-Protein BLAST 2.2.31+

以下是blastp所有参数的详述：
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
   Input file name
   Default = `-'
 -query_loc
   Location on the query sequence in 1-based offsets (Format: start-stop)

 *** General search options
 -task
   Task to execute
   Default = `blastp'
 -db
   BLAST database name
    * Incompatible with:  subject, subject_loc
 -out
   Output file name
   Default = `-'
 -evalue
   Expectation value (E) threshold for saving hits
   Default = `10'
 -word_size =2>
   Word size for wordfinder algorithm
 -gapopen
   Cost to open a gap
 -gapextend
   Cost to extend a gap
 -matrix
   Scoring matrix name (normally BLOSUM62)
 -threshold =0>
   Minimum word score such that the word is added to the BLAST lookup table
 -comp_based_stats
   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'

 *** BLAST-2-Sequences options
 -subject
   Subject sequence(s) to search
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask
 -subject_loc
   Location on the subject sequence in 1-based offsets (Format: start-stop)
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask, remote

 *** Formatting options
 -outfmt
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1),
    12 = JSON Seqalign output,
    13 = JSON Blast output,
    14 = XML2 Blast output
   
   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)
          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
   When not provided, the default value is:
   'qseqid sseqid 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 =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 =0>
   Number of database sequences to show alignments for
   Default = `250'
    * Incompatible with:  max_target_seqs
 -line_length =1>
   Line length for formatting alignments
   Not applicable for outfmt > 4
   Default = `60'
 -html
   Produce HTML output?

 *** Query filtering options
 -seg
   Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
   'no' to disable)
   Default = `no'
 -soft_masking
   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
   Restrict search of database to list of GI's
    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
   subject_loc
 -seqidlist
   Restrict search of database to list of SeqId's
    * Incompatible with:  gilist, negative_gilist, remote, subject,
   subject_loc
 -negative_gilist
   Restrict search of database to everything except the listed GIs
    * Incompatible with:  gilist, seqidlist, remote, subject, subject_loc
 -entrez_query
   Restrict search with the given Entrez query
    * Requires:  remote
 -db_soft_mask
   Filtering algorithm ID to apply to the BLAST database as soft masking
    * Incompatible with:  db_hard_mask, subject, subject_loc
 -db_hard_mask
   Filtering algorithm ID to apply to the BLAST database as hard masking
    * Incompatible with:  db_soft_mask, subject, subject_loc
 -qcov_hsp_perc
   Percent query coverage per hsp
 -max_hsps =1>
   Set maximum number of HSPs per subject sequence to save for each query
 -culling_limit =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 0 and <0.5)>
   Best Hit algorithm overhang value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -best_hit_score_edge 0 and <0.5)>
   Best Hit algorithm score edge value (recommended value: 0.1)
    * Incompatible with:  culling_limit
 -max_target_seqs =1>
   Maximum number of aligned sequences to keep
   Not applicable for outfmt <= 4
   Default = `500'
    * Incompatible with:  num_descriptions, num_alignments

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

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

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

 *** Miscellaneous options
 -parse_deflines
   Should the query and subject defline(s) be parsed?
 -num_threads =1>
   Number of threads (CPUs) to use in the BLAST search
   Default = `1'
    * Incompatible with:  remote
 -remote
   Execute search remotely?
    * Incompatible with:  gilist, seqidlist, negative_gilist, subject_loc,
   num_threads
 -use_sw_tback
   Compute locally optimal Smith-Waterman alignments?