Towards characterizing the solution space of the 1-Dollo Phylogeny problem
Xie, Shunping
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https://hdl.handle.net/2142/104916
Description
Title
Towards characterizing the solution space of the 1-Dollo Phylogeny problem
Author(s)
Xie, Shunping
Issue Date
2019-04-25
Director of Research (if dissertation) or Advisor (if thesis)
El-Kebir, Mohammed
Department of Study
Computer Science
Discipline
Computer Science
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Keyword(s)
1-Dollo phylogeny
Skeleton
Enumeration algorithm
Abstract
Cancer cells may mutate multiple times, from a normal state to a mutated state and vice versa. Given our sequenced data, we can model the mutation process with a phylogenetic tree. One representative model is the k-Dollo parsimony, where all observed mutations mutate from a single normal cell and each character of a cell is gained at most once and lost at most k times. We examine the 1-Dollo Phylogeny problem, does a 1-Dollo phylogeny, a tree that follows the 1-Dollo parsimony model, exist for the observations.
Current algorithms to solve the 1-Dollo Phylogeny problem only tell us whether or not a set of observations has a 1-Dollo phylogeny by outputting a single solution. We explore the structure of 1-Dollo phylogenies and use our idea of a skeleton to develop an algorithm that enumerates all 1-Dollo phylogenies for any set of observations. This algorithm runs much faster than the naive brute force enumeration algorithm for random input. The implementation is here: https://github.com/sxie12/skeleton_solver.
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