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Reconstruction of Strings Past. C. N. Yee and L. Allison * .

Summary: Reconstruction of Strings Past.
C. N. Yee and L. Allison * .
Department of Computer Science,
Monash University,
Australia 3168.
Nov 1991.
Revised May 1992.
uucp: xxx@cs.monash.edu.au xxx=[cyee, lloyd]
Partly supported by Australian Research Council grant A49030439.
* to whom correspondence should be sent.
Summary. A major use of string­alignment algorithms is to compare macro­molecules that are thought to
have evolved from a common ancestor to estimate the duration of, or the amount of mutation in, their
separate evolution and to infer as much as possible about their most recent common ancestor. Minimum
Message Length encoding, a method of inductive inference, is applied to the string­alignment problem. It
leads to an alignment method that averages over all alignments in a weighted fashion. Experiments
indicate that this method can recover the actual parameters of evolution with high accuracy and over a wide
range of values whereas the use of a single optimal alignment gives biased results.
Keywords: alignment, evolution, minimum message length encoding, MML, string similarity.
1. Introduction.
String­alignment algorithms are used to compare macro­molecules, that are thought to be related, to


Source: Allison, Lloyd - Caulfield School of Information Technology, Monash University


Collections: Computer Technologies and Information Sciences