There is increasing interest in, and use of, Optimal Matching techniques in sequence analysis. In recent years especially, both the uses and the software tools that enable this type of analysis have multiplied. Taking up Abbott’s inheritance, many scholars have continued with epistemological and methodological analysis of the application of OM to the social sciences. Nevertheless, many criticisms and doubts have been raised concerning the capacity of the technique to capture common patterns of sequences. Diverse epistemological, methodological and technical questions are awaiting answers. Among the numerous problems one, which has not yet been noticed, concerns the interaction effects between OM elementary operations. This article discusses the interaction effect between indel and substitution costs in Optimal Matching Analysis (henceforth OMA). By means of a simulation based on the eight sequences obtained as element permutation of a binary string of length 3, it will show that varying the substitution and indel costs produces inconsistent results. The article will also show that the sequence patterns obtained from analysis of the distances matrix do not depend on the real existence of common patterns of sequences; rather, they are the result of the interaction effects between the elementary operations of substitution and indel.

OM matters: the interaction effects between indel and substitution costs

Bison, Ivano
2009

Abstract

There is increasing interest in, and use of, Optimal Matching techniques in sequence analysis. In recent years especially, both the uses and the software tools that enable this type of analysis have multiplied. Taking up Abbott’s inheritance, many scholars have continued with epistemological and methodological analysis of the application of OM to the social sciences. Nevertheless, many criticisms and doubts have been raised concerning the capacity of the technique to capture common patterns of sequences. Diverse epistemological, methodological and technical questions are awaiting answers. Among the numerous problems one, which has not yet been noticed, concerns the interaction effects between OM elementary operations. This article discusses the interaction effect between indel and substitution costs in Optimal Matching Analysis (henceforth OMA). By means of a simulation based on the eight sequences obtained as element permutation of a binary string of length 3, it will show that varying the substitution and indel costs produces inconsistent results. The article will also show that the sequence patterns obtained from analysis of the distances matrix do not depend on the real existence of common patterns of sequences; rather, they are the result of the interaction effects between the elementary operations of substitution and indel.
Bison, Ivano
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11572/76956
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