Blastall may be used to perform all five flavors of blast comparison. One
may obtain the blastall options by executing 'blastall -' (note the dash). A
typical use of blastall would be to perform a blastn search (nucl. vs. nucl.) 
of a file called QUERY would be:

blastall -p blastn -d nr -i QUERY -o out.QUERY

The output is placed into the output file out.QUERY and the search is performed
against the 'nr' database.  If a protein vs. protein search is desired,
then 'blastn' should be replaced with 'blastp' etc.

Some of the most commonly used blastall options are:

blastall   arguments:

  -p  Program Name [String]

        Input should be one of "blastp", "blastn", "blastx", "tblastn", or "tblastx".

  -d  Database [String]
    default = nr

        The database specified must first be formatted with formatdb.
        Multiple database names (bracketed by quotations) will be accepted.
        An example would be

                -d "nr est"

        which will search both the nr and est databases, presenting the results as if one
        'virtual' database consisting of all the entries from both were searched.   The
        statistics are based on the 'virtual' database of nr and est.  

  -i  Query File [File In]
    default = stdin

        The query should be in FASTA format.  If multiple FASTA entries are in the input
        file, all queries will be searched.

  -e  Expectation value (E) [Real]
    default = 10.0

  -o  BLAST report Output File [File Out]  Optional
    default = stdout

  -F  Filter query sequence (DUST with blastn, SEG with others) [String]
    default = T

         BLAST 2.0 and 2.1 uses the dust low-complexity filter for blastn and seg for the
         other programs. Both 'dust' and 'seg' are integral parts of the NCBI toolkit
         and are accessed automatically.

         If one uses "-F T" then normal filtering by seg or dust (for blastn)
         occurs (likewise "-F F" means no filtering whatsoever).  

         This options also takes a string as an argument.  One may use such a 
         string to change the specific parameters of seg or invoke other filters.
         Please see the "Filtering Strings" section (below) for details.

  -S  Query strands to search against database (for blast[nx], and tblastx).  3 is both, 1 is top, 2 is bottom [Integer]
    default = 3

  -T  Produce HTML output [T/F]
    default = F

  -l  Restrict search of database to list of GI's [String]  Optional

        This option specifies that only a subset of the database should be
        searched, determined by the list of gi's (i.e., NCBI identifiers) in a 
        file.  One can obtain a list of gi's for a given Entrez query from .
        This file should be in the same directory as the database,
        or in the directory that BLAST is called from.

  -U  Use lower case filtering of FASTA sequence [T/F]  Optional
    default = F

        This option specifies that any lower-case letters in the input FASTA file
        should be masked.  


A new option has been added to search multiple queries at once for the
blastn and tblastn program options of blastall.

  -B Number of concatenated queries, for blastn and tblastn [Integer]
     default = 0

This new feature similar in principle, but different in implementation
from the support for multiple queries already existing in megablast.
The combination of ungapped search (-g F)  and multiple queries
(-B N) is not supported. The argument to -B option must be equal
to the number of sequences in the FASTA input file.

Processing multiple query sequences in one run can be much faster than
processing them with separate runs because the database is scanned only 1
time for the entire set of queries. When the -B option is used, the
results may differ from the ones produced with individual queries. Usually
results  will be at least as good or better (in terms of score/evalue)
than the results of corresponding  individual queries; exceptions  occur
due to the heuristic nature of BLAST. Additional alignments may appear.
It is  guaranteed that matching sequences will
appear in the same order when they are tied in evalue
and are part of the output both with and without -B.
When the -B option is used, the summary statistics at the bottom
of the output are for the combined set of queries; at present,
the summary statistics are not tabulated for the individual
queries in a multiple-query input.