For Wednesday:

• Review questions
  
• Takehome quiz 8 due before class
• Study guide questions on positive selection will be posted

Microarray questions

figure here, and here (old slides)

Discuss positive selection (MrBayes/Paml) ppt here

SUMP - SUMT commands (MrBayes build in alternative to excel)

Ratio of non-synonymous to synonymous substitutions (called omega in MrBayes):

=1 no selection evident (only true for pseudogenes)

<1 purifying selection (normal for most genes - maybe selection against detrimental characteristics is sufficient)

>1 positive or diversifying selection. (E.g., sites interacting with immune system, change selected (fixed in population) because it provided a benefit.)

• Import file(s)
• calculate average P(omega>1) for all columns
• Plot P(omega>1) along sequence
• Calculate histogram for omega<1 (omega- column)
• Calculate 95% credibility interval for omega<1

Course Evaluation