Spidey Parameter

    SPIDEY   arguments:

  -i  Input file -- genomic sequence(s) [File In]
  -m  Input file -- mRNA sequence(s) [File In]
  -p  Print alignment? 0=summary+alignments, 1=summary, 2=alignments, 3=summary&alignments in different files [Integer]  Optional
    default = 0
  -o  Output file 1 (summary or summary+aln) [String]  Optional
    default = stdout
  -a  Output file 2 (alignments) [String]  Optional
    default = spidey.aln
  -G  Input file is a GI list [T/F]  Optional
    default = F
  -n  Number of gene models [Integer]  Optional
    default = 1
  -r  Organism (genomic sequence) v=vertebrate,
d = drosophila, p = plant, c = C. elegans, m = Dictyostelium discoideum [String]  Optional
    default = v
  -e  First-pass e-value [Real]  Optional
    default = 0.0000000001
  -f  Second-pass e-value [Real]  Optional
    default = 0.001
  -g  Third-pass e-value [Real]  Optional
    default = 10
  -c  % identity cutoff [Integer]  Optional
    default = 0
  -l  % length coverage cutoff [Integer]  Optional
    default = 0
  -s  interspecies alignment [T/F]  Optional
    default = F
  -j  Print ASN.1 alignment? [T/F]  Optional
    default = F
  -k  File for asn.1 [String]  Optional
    default = spidey.asn
  -w  Is the input mRNA masked (lowercase)? [T/F]  Optional
    default = F
  -d  Fetch the CDS and compute its results also? [T/F]  Optional
    default = F
  -t  File with feature table [File In]  Optional
  -F  Start of genomic interval desired (from) [Integer]  Optional
    default = 0
  -T  Stop of genomic interval desired (to) [Integer]  Optional
    default = 0
  -u  Make a multiple alignment of all input mRNAs [T/F]  Optional
    default = F
  -X  Use extra-large intron sizes [T/F]  Optional
    default = F
  -L  The extra-large intron size to use [Integer]  Optional
    default = 220000
  -S  Restrict to plus (p) or minus (p) strand of genomic seq? [String]  Optional
  -M  File with donor splice matrix [File In]  Optional
  -N  File with acceptor splice matrix [File In]  Optional
  -R  File (including path) to repeat blast database for filtering [String]  Optional