[EMBOSS] esim4 man page

[Derek Gatherer]

Hi

Is there an esim4 man page?

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/index.html

The rest of EMBASSY is above, but not esim4.  The original sim4 has a quick 
help list, but I wondered if there is any extra functionality in the 
EMBASSY version.

Cheers
Derek

 > sim4
sim4 seq1 seq2_db [[WXKCRDHAPNBS]=]

        W  -  word size. (W=12)
        X  -  value for terminating word extensions. (X=12)
        K  -  MSP score threshold for the first pass. (e.g., K=16)
        C  -  MSP score threshold for the second pass. (e.g., C=12)
        R  -  direction of search; 0 - search the '+' (direct) strand only;
              1 - search the '-' strand only; 2 - search both strands and
              report the best match. (R=2)
        D  -  bound for the range of diagonals within consecutive msps in an
              exon. (D=10)
        H  -  weight factor for MSP scores in relinking. (H=500)
        A  -  output format: exon endpoints only (A=0), alignment text (A=1),
              alignment in lav (block) format (A=2), or both exon endpoints
              and alignment text (A=3, A=4). If complement match, A=0,1,2,3
              give direct positions in the long sequence and complement
              positions in the short sequence. A=4 gives direct positions in
              the first sequence, regardless of the relative lengths.
              A=5 prints the exon and CDS coordinates (the latter, if known)
              in the `exon file' format required by PipMaker. To be used
              with full-length mRNA sequences.
        P  -  if not 0, remove poly-A tails; report coordinates in the
              '+' (direct) strand for complement matches; use lav alignment
              headers in all display options. (P=0)
        N  -  accuracy of sequences (non-zero for highly accurate). (N=0)
        B  -  if 0, dis-allow ambiguity codes (other than N and X) in the
              sequence data. (B=1)
        S  -  coding region specification (available only with A=5);
              format: S=n1..n2