Math 660: Advanced Mathematical Modeling (Theory of Phylogenetics)

Spring 2009

To contact the instructors:

e.allman@uaf.edu

j.rhodes@uaf.edu

Course syllabus: M660syl.pdf

Paup manual (c.1993, so only covering parsimony) Paup_Doc_31.pdf

Homework Assignments:

The dates below are when problems were assigned. Unless otherwise noted, problems are always due the following Tuesday.

• 1/27 -- 1/29 read Chapters 1, 2 of notes, do problems §2.6, # 1-6,11; read Chapter 3 of Felsenstein     selected solutions
• 2/3 -- 2/5 read Chapter 3 of notes (proof of Theorem 8 for math-oriented folks) , do problems §3.8, #1-4, 8, 9, 14, 18, 20, 23; Read Chapters 1 and 2 (p.11-16 only) of Felsenstein
• 2/10 -- 2/12 read Chapter 5 of notes, do problems §5.5, # 1-3, 5-8, 14, 23-25; Read 1993 PAUP manual and/or Felsensetin Chapter 7 for fun
• 2/17 -- 2/19 This week's assignment will be due on Thursday 2/26 and assigned on Thursday of this week.
          For starters: Optional background reading on Probability: Chapter 4, Sections 2 and 3 from Allman/Rhodes
          Read Chapter 6 of notes, do problems § 6.5, # 2, 7, 14; Handout with PAUP* exercises due Tuesday 3/3. Requires dataset: primates-mtDNA.nex
           PAUP* solutions
• 2/24 --2/26 Continue reading Chapter 6 of notes, do problems § 6.5, #1, 3-5, 17, 21, 23
• 3/3 --3/5 Read Chapter 7
• BREAK
• 3/19 Midterm Exam solutions
• 3/24 --3/26 do problems § 7.4, # 1-3, 5-7; read Chapter 8, do problems § 8.5, #1, 2, 8
• 3/31 -- 4/2 do problem § 8.5, # 10; read Chapter 9, do problems § 9.5, #2-5, 7
• 4/7 -- 4/9 read Chapter 10, do problems § 10.4, #1-5
• 4/14 -- 4/16 Handout with PAUP* exercises, requires datasets: insects.nex, sim-data1.nex, sim-data2.nex
• 4/21 -- 4/23 read Chapter 11, do problem § 11.6, 1, 2(p_3 only), 3(p_1-p_3 only)