[BMI776] BMI776 notes

[Colin Dewey]

Hi BMI 776ers,

Just a couple of notes on the homework, readings:

- For HW #1, the convention is that branch lengths on trees are the  
expected number of mutations *per site*.  I have added "per site" to  
question #1, to make this clear.

- For HW #1, although I gave you a fixed tree, I would prefer that  
you write your algorithms in a generic way, able to work on any tree  
topology.  A fixed tree was given because I didn't want you to have  
to read and parse a tree structure from a file (which can be  
painful).  Writing your algorithms generically now will likely save  
you trouble later on in the semester.

- Readings: I have posted the readings for next week.  Most of you  
have read the assigned text sections in 576.  For those of you who  
haven't, please make sure you get up to speed on Markov chains and HMMs.

Let me know if you have questions.

- Colin