Electrical Engineering
      and Computer Sciences

Electrical Engineering and Computer Sciences

COLLEGE OF ENGINEERING

UC Berkeley

A Minimum Spanning Tree Framework for Inferring Phylogenies

Daniel Giannico Adkins

EECS Department
University of California, Berkeley
Technical Report No. UCB/EECS-2010-157
December 15, 2010

http://www.eecs.berkeley.edu/Pubs/TechRpts/2010/EECS-2010-157.pdf

This dissertation discusses how to write efficient, deterministic programs to infer phylogenetic trees. These programs are based on a theoretically optimal polynomial time algorithm. The programs are practical and efficient. The problem is to infer phylogenetic trees from sequence data at the leaves. Likelihood approaches attempt to solve an NP-complete optimization problem, and are computationally intense. Our approach is to apply efficient, polynomial time algorithms which are provably accurate to within a constant factor of optimal. We present a program which is practical and computationally efficient.

Advisor: Satish Rao


BibTeX citation:

@phdthesis{Adkins:EECS-2010-157,
    Author = {Adkins, Daniel Giannico},
    Title = {A Minimum Spanning Tree Framework for Inferring Phylogenies},
    School = {EECS Department, University of California, Berkeley},
    Year = {2010},
    Month = {Dec},
    URL = {http://www.eecs.berkeley.edu/Pubs/TechRpts/2010/EECS-2010-157.html},
    Number = {UCB/EECS-2010-157},
    Abstract = {This dissertation discusses how to write efficient, deterministic programs to infer phylogenetic trees.  These programs are based on a theoretically optimal polynomial time algorithm.  The programs are practical and efficient.

The problem is to infer phylogenetic trees from sequence data at the leaves.  Likelihood approaches attempt to solve an NP-complete optimization problem, and are computationally intense.

Our approach is to apply efficient, polynomial time algorithms which are provably accurate to within a constant factor of optimal.

We present a program which is practical and computationally efficient.}
}

EndNote citation:

%0 Thesis
%A Adkins, Daniel Giannico
%T A Minimum Spanning Tree Framework for Inferring Phylogenies
%I EECS Department, University of California, Berkeley
%D 2010
%8 December 15
%@ UCB/EECS-2010-157
%U http://www.eecs.berkeley.edu/Pubs/TechRpts/2010/EECS-2010-157.html
%F Adkins:EECS-2010-157