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Rambaut A. and Grassly N. C.
Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees.
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A. Bairoch.
The PROSITE dictionary of sites and patterns in proteins, its current status.
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B.A. Butler.
Sequence analysis using gcg.
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E. Coward.
Shufflet: Shuffling sequences while conserving the $ k$-let counts.
Bioinformatics, (15):1058-1059, 1999.

A. Denise, O. Roques, and M. Termier.
Random generation of words of context-free languages according to the frequencies of letters.
In D. Gardy and A. Mokkadem, editors, Mathematics and Computer Science: Algorithms, Trees, Combinatorics and probabilities, Trends in Mathematics, pages 113-125. Birkhaüser, 2000.

R. Durbin, S. R. Eddy, A. Krogh, and G. Mitchison.
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Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., and Bairoch A.
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Nucleic Acids Res., (31):3784-3788, 2003.

P. Flajolet, P. Zimmermann, and B. Van Cutsem.
A calculus for the random generation of labelled combinatorial structures.
Theoretical Computer Science, 132:1-35, 1994.
A preliminary version is available in INRIA Research Report RR-1830.

Reinert G., Schbath S., and Waterman M.S.
Probabilistic and statistical properties of words: An overview.
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M. Nebel.
Combinatorial properties of rna secondary structures.
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Y. Ponty.
Etudes combinatoire et génération aléatoire des structures secondaires d'ARN.
Master's thesis, Université Paris Sud, 2003.
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D.B. Searls.
Formal language theory and biological macromolecules.
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Yann Ponty 2007-04-19