Davenport-Schinzel sequences and their geometric applications
Davenport-Schinzel sequences and their geometric applications
Optimal parametric search on graphs of bounded tree-width
Journal of Algorithms
Maximum likelihood on four taxa phylogenetic trees: analytic solutions
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
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We present efficient sensitivity-analysis algorithms for two problems involving Markov models of sequence evolution: ancestral reconstruction in evolutionary trees and local ungapped alignment under log-odds scoring. Our algorithms generate complete descriptions of the optimum solutions for all possible values of the evolutionary distance. The running time for the parametric ancestral reconstruction problem under the Kimura 2-parameter model is O(kn + kn2/3 log k), where n is the number of sequences and k is their length, assuming all edges have the same length. For the parametric gapless alignment problem under the Jukes-Cantor model, the running time is O(mn + mn2/3 log m), where m and n are the sequence lengths and n ≤ m.