@inproceedings{64c99e7b4b17439d91f8c17c654da77c,

title = "Estimating the deviation from a molecular clock",

abstract = "We address the problem of estimating the degree to which the evolutionary history of a set of molecular sequences violates a strong molecular clock hypothesis.We quantify this deviation formally, by defining the “stretch” of a model tree with respect to the underlying ultrametric tree (indicated by time). We then define the “minimum stretch” of a dataset for a tree and show how this can be computed optimally in polynomial time. We also present a polynomial-time algorithm for computing a lower bound on the stretch of a given dataset for any tree. We then explore the performance of standard techniques in systematics for estimating the deviation of a dataset from a molecular clock. We show that standard methods, whether based upon maximum parsimony or maximum likelihood, can return infeasible values (i.e. values for the stretch which cannot be realized on a tree), and often under-estimate the true stretch. This suggests that current approximations of the degree to which data sets deviate from a molecular clock may significantly underestimate these deviations. We conclude with some suggestions for further research.",

author = "Luay Nakhleh and Usman Roshan and Lisa Vawter and Tandy Warnow",

year = "2002",

doi = "10.1007/3-540-45784-4_22",

language = "English (US)",

isbn = "3540442111",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "287--299",

editor = "Roderic Guigo and Dan Gusfield",

booktitle = "Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings",

address = "Germany",

note = "2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 ; Conference date: 17-09-2002 Through 21-09-2002",

}