Towards characterizing the solution space of the 1-Dollo Phylogeny problem

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.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Computer Science

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2019

Author dc:creator

• Xie, Shunping

Contributors dc:contributor

• El-Kebir, Mohammed

• 1-Dollo phylogeny
• Skeleton
• Enumeration algorithm

Statement dc:rights

• Copyright 2019 Shunping Xie

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/104916

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/104916