Gumbel parameters for sequence alignment statistics

The NCBI Gumbel parameters library computes Gumbel parameters for an
arbitrary scoring matrix and gap penalties. It also includes P-values
calculation using a new more accurate finite size correction method.
The parameters can be used for Basic Local Alignment Search Tool (BLAST).
Parameters for a gapless scoring scheme can be calculated as an option.

References
1. Park, Y., Sheetlin, S. and Spouge, J.L. (2005) Accelerated convergence
and robust asymptotic regression of the Gumbel scale parameter for gapped
sequence alignment. Journal of Physics A: mathematical and general, 38,
97-108.
2. Sheetlin, S., Park, Y. and Spouge, J.L. (2005) The Gumbel pre-factor k
for gapped local alignment can be estimated from simulations of global
alignment. Nucleic Acids Research, 33, 4987-4994.
3. Park, Y., Sheetlin, S. and Spouge, J.L. (2009) Estimating the Gumbel
Scale Parameter for Local Alignment of Random Sequences by Importance
Sampling with Stopping Times. Annals of Statistics.
4. Park, Y., Sheetlin, S. and Spouge, J.L. (2009) On-line computation of
statistical parameters for local alignment score distribution. In
preparation.

Additional information can be found here:
http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html.ncbi/blast/index.html