Homework for CS 581, Fall 2020
Homework policies
Due date:
All homework is due at 10 PM on the due date, via Moodle (unless
otherwise specified).
Late homeworks (up to 48 hours late) can be accepted for reduced
credit:
80% if within 24 hours and 60% if within 48 hours.
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.
Disputing a grade:
Please come see me directly if you have questions
or concerns about how your homework was graded.
Grading policy:
The homework overall contributes 40% of the course grade,
and each homework (unless otherwise specified) contributes the same amount.
The worst hw grade is dropped.
Assignments
- Homework 1. Due Thursday, September 3, 10 PM.
- Read Chapters 1-3, 5.1-5.5.
- HW problems:
-
Chapter 1: problems 1, 5, 8. Also do one of 10 and 11.
-
Chapter 2: problems 21, 29, and 32.
-
Chapter 3: problems 3 and 5
-
Homework 2. Due Thursday, September 10, 10 PM
- Read Chapters 4, 5.6-5.11, 8.1-8.2, 8.4-8.5, 8.8
- HW problems:
-
Chapter 4 problems 1, 5, 6, 17.
-
Chapter 5 problems 7, 9, 12, 18.
-
Chapter 8 problems 7-9.
-
Homework 3. Due Thursday, September 17, 10 PM (Note: for this homework, you
are strongly encouraged to pair up with someone else to do the work that has to do with running analyses (not the review questions). Just make sure you write it up yourself, and you write down the name of anyone
you worked with in your submitted homework.
Your submitted homework should be properly formatted PDF based preferably on
laTex, but Word is allowed.)
- Read: Chapter 8.6, 8.7, 8.9-8.13, Chapter 10.1-10.7, and Appendix C
- Answer all the review questions from Chapters 1, 4, 5, and 8 (no need to write these down, but be prepared to answer them in class).
- (Note: you will need to get help from Vlad for this assignment, even to find the datasets! Please check with him and probably check the Slack channel.) Analyze simulated datasets from 1000M1 and 1000M4 (see this webpage), using the true alignment, using
at least two of the following sets of methods, and record the average FN and FP error rates across the model conditions.
Write up your results sufficiently for the experiment you did to be reproducible
(i.e., method version numbers and commands).
Comment on: what did you expect to see? What did you see?
What did you learn?
Include properly cited references for any software that you use.
- Neighbor Joining, using two of the following ways of calculating distances: logdet distances, Jukes-Cantor distances, and p-distances
- Balanced Minimum Evolution within FastME, using the same distances as for the previous question
- UPGMA using p-distances
- RAxML or IQTree, under both the GTR and JC models
- FastTree2, under both the GTR and JC models
- Any other tree estimation method you wish (e.g., maximum parsimony, or
some quartet-based method).
- Homework 4. Due Thursday, September 24, 10 PM.
- Read Chapters 6.1-6.2, 7.1-7.7, 9.1-9.7.
- Review questions (please do them, even though they
will not be graded): Chapter 6(1), 7(1)-(7), 9(1)-(7).
-
HW problems: Chapter 6 problems 2-4, Chapter 7 problems 1 and 2, and
Chapter 9 problems 3 and 4.
-
Homework 5. Due Thursday, October 1, 10 PM.
- Read Chapter 9.8-9.20 and
"Phylogeny Estimation Given Sequence Length Heterogeneity." In press, Systematic Biology, (HTML).
-
HW problems: Chapter 9 problems 10 and 11.
-
Data analysis (do this by yourself):
Pick two of the following multiple
sequence alignment methods: MAFFT, Clustal-Omega, Regressive, PASTA, Muscle,
and UPP (Vlad will help you find these methods).
Perform the following analyses on
10 of
the 20 1000M1 replicates, 10 of the 20 1000M4 replicates, and also 16S.M.
- For each alignment method you picked, use it to
compute a multiple sequence alignment and record the alignment
error (SPFN and SPFP), computed using FastSP.
(Either run the method in a default setting that is appropriate for nucleotide
sequences, or run it in a setting that is supposed to give more accurate results.)
- Compute a tree on the estimated multiple sequence alignment and the
true multiple sequence alignment using
any standard tree estimation method (your choice); record the
FN and FP tree error rate for each analysis.
(Note: for the biological dataset, you need to use the 75% bootstrap
tree on the dataset.)
Write up your results sufficiently for the experiment you did to be reproducible
(i.e., method version numbers and commands).
Comment on: your choice of methods (why?), what did you expect to see, what did you see,
what did you learn, what are you surprised by or confused about?
Include properly cited references for any software that you use.
(Please, no screenshots, and it's best to show commands in the document rather than
in other sites.)
- Homework 6. Due Wednesday October 7, 10 PM.
No late homework allowed.
-
Chapter 6, problem 12.
-
Chapter 7, problem 3.
-
Chapter 8, problem 13.
-
Chapter 10, problems: 3,4, 7, 9, 10.
- Homework 7. Due Thursday October 15, 10 PM.
- Write a 1-2 page document with a proposal for your
course project. You can describe more than one possible
project. This homework is credit, no credit, and will not
affect your homework grade (but does impact your
course participation grade).
- Homework 8. Due Monday October 19, 10 PM.
- Submit single slide (PDF or PPTX) describing your
course
project
idea. You will present your idea in class on Tuesday, October 20.
You will have 5 minutes, with 3 minutes for your presentation and
2 minutes for Q&A.
- Homework 9. Due Monday, October 26, 10 PM. Writing assignment, see
Moodle.
ALSO: questions regarding papers for this week must be
sent by email to Vladimir Smirnov (these count towards class participation),
no later than 10 PM on the night before the paper presentation.
- Homework 10. Due Monday, November 2, 10 PM. Writing assignment, see Moodle.
ALSO: questions regarding papers for this week must be
sent by email to Vladimir Smirnov (these count towards class participation),
no later than 10 PM on the night before the paper presentation.
- Revised course project proposal, due November 6, see Moodle.
- Homework 11. Due Monday, November 9, 10 PM. Writing assignment, see Moodle.
ALSO: questions regarding papers for this week must be
sent by email to the person presenting the paper and cc'd to me and Vladimir Smirnov(these count towards class participation),
no later than 10 PM on the night before the paper presentation.
- Homework 12. Due Monday, November 16, 10 PM. Writing assignment
(based on reading three papers, see Moodle).
Class participation assignments
- Class participation includes submitting and asking questions
for the papers presented in class. The questions must be sent to
Vladimir Smirnov by email, the night before the paper presentation.
-
Your paper presentation is also part of class participation: send your
PPTX or PDF to Tandy Warnow 48 hours before it will be presented.
Course project. Due December 8 at 9 AM. See Moodle.