Bl2seq
------

Bl2seq performs a comparison between two sequences using either the blastn or
blastp algorithm.  Both sequences must be either nucleotides or proteins.
The options may be obtained by executing 'bl2seq -'.

  -i  First sequence [File In]
  -j  Second sequence [File In]
  -p  Program name: blastp, blastn, blastx. For blastx 1st argument should be nucleotide [String]
    default = blastp
  -g  Gapped [T/F]
    default = T
  -o  alignment output file [File Out]
    default = stdout
  -d  theor. db size (zero is real size) [Integer]
    default = 0
  -a  SeqAnnot output file [File Out]  Optional
  -G  Cost to open a gap (zero invokes default behavior) [Integer]
    default = 0
  -E  Cost to extend a gap (zero invokes default behavior) [Integer]
    default = 0
  -X  X dropoff value for gapped alignment (in bits) (zero invokes default behavior) [Integer]
    default = 0
  -W  Wordsize (zero invokes default behavior) [Integer]
    default = 0
  -M  Matrix [String]
    default = BLOSUM62
  -q  Penalty for a nucleotide mismatch (blastn only) [Integer]
    default = -3
  -r  Reward for a nucleotide match (blastn only) [Integer]
    default = 1
  -F  Filter query sequence (DUST with blastn, SEG with others) [String]
    default = T
  -e  Expectation value (E) [Real]
    default = 10.0
  -S  Query strands to search against database (blastn only).  3 is both, 1 is top, 2 is bottom [Integer]
    default = 3
  -T  Produce HTML output [T/F]
    default = F