Homework for CS 581, Spring 2018
Homework policies
Due date:
All homework is due at 2 PM on the due date, via Moodle (unless
otherwise specified).
Late homeworks (up to 48 hours late) can be accepted for reduced
credit (see course webpage for details), except when otherwise
specified (e.g., see Homework 5).
Collaboration policy:
You are expected to write up the homework yourself, but you are
welcome to discuss the homework with other students in the class.
If you discuss the homework with other students, clearly specify this on
your homework.
Reading assignments:
Some homeworks involve homework problems from the textbook, and
many homework assignments involve
reading the textbook or published papers.
The class discussion depends on you doing the reading,
as I will not be teaching all the material.
Review questions:
The textbook has two types of questions: review questions and
homework problems.
In general, I will be assigning problems from the
homework problems and not from the review questions (although
do note that this is not true for some homework assignments).
We may discuss
the review questions in class, so
please look over the review questions as well.
Optional homework:
You are welcome to submit solutions to problems
from the textbook
that interest you.
These won't count towards the grade, but
I'll personally grade them and give you feedback.
I'm recommending some of them in the homework list.
Similarly, you are encouraged to read papers from the
literature (perhaps a paper cited in the textbook), and
write up a discussion of the paper.
If one of the papers really excites you, you might want
to present it in class!
(Everyone has to present a paper, so you could get a head
start on this, by finding a paper you want to present instead
of being assigned one.)
Disputing a grade:
Please come see me directly if you have questions
or concerns about how your homework was graded.
Grading policy:
All weekly homeworks count for 100 points,
and contribute 25% of the course grade.
The worst grade is dropped.
Assignments
 Due Tuesday, January 23, 2018.
 Homework 1. Due Thursday, January 25, 2018.
 HW problems:
Chapter 1 problems 1, 5, and 10.
Chapter 2 problems 1, 5, and 21.
Chapter 3 problems 3 and 22.
 Optional (won't count towards grade):
Chapter 1, problem 11.
Chapter 3, problem 9.
 Homework 2. Due Thursday, February 1, 2018.

Read: Chapter 4

HW problems: Chapter 4, problems 1, 5, 6, and 17

Optional (won't count towards grade): Chapter 4, problem 18

Homework 3.
Due Thursday February 8, 2018.

Read: Chapter 8

HW problems: Chapter 8, problems 8, 9, 13, 14, and 17.

Apply the Sankoff algorithm for maximum parsimony on a fixed tree
(see Chapter 4.3) to the following input:
 Rooted tree T: ((a,e),(b,(c,d)))
 Character states: a=0, b=0, c=1, d=0, e=1
 The cost matrix M has M[0,0]=M[1,1]=0, M[0,1]=2, and M[1,0]=1.
(a) Letting r denote the root of T, compute Cost(r,0) and
Cost(r,1), and show all your calculations.
(b) What is the parsimony score of this input?
 Apply the brute force algorithm to compute
the probability of a site pattern to the following
input:
 CFN Model tree T has topology (a,(b,(c,d))).
The edge above the LCA of (c,d) has substitution
probability 0.4, and all other edges have substitution
probability 0.01.
 Character states: a=0, b=0, c=1, d=1.
(a) Compute the probability of this site pattern on this tree.
Show all your work.
(b) Is there another site pattern that has higher probability?
If so, find it  and otherwise explain why you think
there isn't such a site pattern.

Optional (won't count towards grade): Chapter 8, problem 18

Due Tuesday, February 13, 2018.

Homework 4.
Due Thursday, February 15, 2018.
 Read Chapters 9.19.5.

HW problems: Chapter 9, problems 1, 3, and 4

Homework 5.
Due Thursday, February 22, 2018.

Read Chapter 9.69.16 and Appendix C.

Read the following papers. For each paper, write a brief summary (2 paragraphs, maximum) and pose two questions or critiques. The two questions can either be requests for clarification, a critique of the paper (of the methodology or conclusions), or a suggestion for followup research.
Pay close attention to the methodology used to evaluate the methods that are presented.
Be prepared to discuss the papers in class.

"Who watches the watchmen?", by Iantorno et al. (2014), DOI 10.1007/9781627036467_4

"PhylogenyAware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis", by Loytynoja and Goldman (2008), DOI: 10.1126/science.1158395

"Fast, scalable generation of highquality protein multiple sequence alignments using Clustal Omega" by Sievers et al. (2011), DOI: 10.1038/msb.2011.75

"BAliPhy: simultaneous Bayesian inference of alignment and phylogeny",
by Suchard and Redelings (2006), DOI: 10.1093/bioinformatics/btl175

"MCoffee: combining multiple sequence alignment methods with TCoffee" (2006) by Wallace et al. DOI: 10.1093/nar/gkl091.

"SplitInducing Indels in Phylogenomic Analysis by Donath and Stadler (2011)
(PDF)
(retrieved from Semantic Scholar)

HW problems:
Chapter 9, problems 11 and 13.

Due Tuesday, February 27, 2018.

Read Chapters 6.16.2, 10.110.4.

Homework 6.
Due Thursday, March 1, 2018.
 Read Chapter 10.5.
 Chapter 6, Review question 1.
 Chapter 6, Homework problems 4 and 8.
 Submit a 2page critique of the paper by Donath
and Stadler (from February 22, 2018 list of papers).
 Submit a 2page critique of any other paper
from the February 22 list of papers.

Due Tuesday, March 6, 2018.

Homework 7.
Due Thursday, March 8, 2018.
 Chapters 7 and 10, all review questions.
 HW problems: Chapter 7, problem 2. Chapter 10, problems 1 and 2.
 Select two papers that are
closely related to your final project proposal, and
write a 35 page review of the papers where you discuss
what they agree on, what they differ on, and what they leave
open. Make sure to critique the two papers carefully.
Your review should have full citations and format, and
will be evaluated not only for content but also for writing
(i.e., correct all spelling, grammar, and punctuation).

Due March 9 (Friday):

12 page proposal for your final project (noon, via Moodle).

Make an appointment to meet with me in person to discuss
your ideas
before you submit the proposal.

Meet with me again after I have given you feedback about
the proposal.

Homework 8.
Due March 15 (Thursday).

Read Chapter 5.15.11.

Do all review questions from Chapter 5.

Do problems 9, 12, 15, 16, and 18
from Chapter 5.
 Due March 16 (Friday).

Approved final project proposal (by noon, via Moodle)