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An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree.. Pacific Symposium on Biocomputing, page 179-190. (2001)Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model., , and . PLoS Comput. Biol., (2006)Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases., , and . PLoS Comput. Biol., (2022)A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny, , and . PLoS Comput Biol, 6 (8): e1000868+ (Aug 5, 2010)Frnakenstein: multiple target inverse RNA folding, , , , , and . BMC Bioinformatics, 13 (1): 260+ (Oct 9, 2012)A nucleotide substitution model with nearest-neighbour interactions., and . ISMB/ECCB (Supplement of Bioinformatics), page 216-223. (2004)Combining statistical alignment and phylogenetic footprinting to detect regulatory elements., , and . Bioinform., 24 (10): 1236-1242 (2008)a heuristic method to reconstruct the history of sequences subject to recombinaison. Journal of Molecular Evolution, (1993)Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks., and . WABI, volume 2812 of Lecture Notes in Computer Science, page 287-302. Springer, (2003)Comparison of Coding DNA., , and . CPM, volume 1448 of Lecture Notes in Computer Science, page 153-173. Springer, (1998)