METHODS OF PHYLOGENY RECONSTRUCTION

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Dean Zeller Department of Computer Science
METHODS OF PHYLOGENY RECONSTRUCTION
BINARY TWO-SPECIES TEST (BTST)
GOALS OF RESEARCH

• Test returns 1 if species x and y are genetically
  close to a certain degree, and 0 otherwise.
• Step 1 Collect data to form an edge grid.
• Step 2 Create k-leaf power by connecting
  appropriate edges.
• Step 3 Reconstruct phylogeny using Brandstädt
  and Les algorithm (2005).

• Create methods of phylogeny reconstruction from
  various hypothetical tests.
• Create more adequate evolution models.
• Create teachable lessons on bioinformatics
  suitable for a mid-level computer science,
  mathematics, or biology class.
• Discover methods of phylogeny reconstruction from
  a new perspective.

BACKGROUND EVOLUTION TREES
the great Tree of Life fills with its dead and
broken branches the crust of the earth, and
covers the surface with its ever-branching and
beautiful ramifications. Charles Darwin
(1809-1882)

• Notes
• Linear time solution for 3- and 4-leaf roots.
• An open problem for k ? 5.
• Severely limits analysis capabilities.

DISCRETE TWO-SPECIES TEST (DTST)

• Test returns a discrete value (k2,3,4,)
  denoting a distance from x to y.
• Step 1 Collect data to form a distance grid.
• Step 2 Create k-leaf powers incrementally.
• Step 3 Reconstruct phylogeny in same order.

Step 2 k-leaf powers
k?2
k?3
k?4
CLASS ASSIGNMENTS

• Assignment 1 Drawing Trees
• Assignment 2 Phylogenetic Distance Graphs
• Assignment 3 Phylogeny Reconstruction
• (Tested on CS10051 students, Spring 2006)

Step 3 Phylogenies/k-leaf roots
Contact Dean Zeller, dzeller_at_cs.kent.edu