"The complete parsimony haplotype inference problem and algorithms based on integer programming, branch-and-bound and Boolean satisfiability" by Gerold Jäger

Faculty Selected Works of Sharlee Climer

Article

The complete parsimony haplotype inference problem and algorithms based on integer programming, branch-and-bound and Boolean satisfiability

Journal of Discrete Algorithms (2016)

Gerold Jäger, Umeå University
Sharlee Climer, Washington University in St. Louis
Weixiong Zhang, Washington University in St. Louis

Link

Abstract

Haplotype inference by pure parsimony (Hipp) is a well-known paradigm for haplotype inference. In order to assess the biological significance of this paradigm, we generalize the problem of Hipp to the problem of finding all optimal solutions, which we call Chipp. We study intrinsic haplotype features, such as backbone haplotypes and fat genotypes as well as equal columns and

Keywords

Haplotype inference,
Pure parsimony,
Branch-and-bound,
Integer programming,
Boolean satisfiability

Disciplines

Publication Date

March 1, 2016

DOI

10.1016/j.jda.2016.06.001

Citation Information

Gerold Jäger, Sharlee Climer and Weixiong Zhang. "The complete parsimony haplotype inference problem and algorithms based on integer programming, branch-and-bound and Boolean satisfiability" Journal of Discrete Algorithms Vol. 37 (2016) p. 68 - 83
Available at: http://works.bepress.com/sharlee-climer/1/