Discussion of midterm (go over additional questions on home page).
Tree of life - three domains, main endosymbiosis events, archaeplastida, other algae.
Black queen hypothesis (figure)

Why is %identity not a good measure for the significance of blast hits? See blast output and histograms in demo file.

• How are new genes are created? How can genome size increase? Everyone should have at least three distinct mechanisms.

• Discussion of The Evolutionary Fate and Consequences of Duplicate Genes
  
  What is the most frequent outcome of a gene duplication?
  What is the most frequent outcome, in case the gene doesn't undergon non-functionalization?
  What does any of this have to do with building up a post mating hyybrization barrier?
  Aside: How can genes be duplicated?
  

Aditional slides on human evolution and archaic admixture.

Discuss terms used in cladistics - rooted versus unrooted (clades versus clanns), homoplasies, monophyletic, paraphyletic, polyphyletic, Ashlock's holophyly

 

example of simple perl scripts:

• (perl script to extract top scoring hits is here (pdf)-- extra credit: how would you modify the script, to print out not only the first reported match for a query, but all hits that have equally good E-values to the first one? Note: in Perl the operator for "logical and" is && and "not equal" for a number is != and "not equal" for a string is ne)
• (perl script to replace gi number with position on the genome is here (pdf) (faa_sample, feature_table sample)

• How would a misplaced origin of replication look like in two similar genomes?
• Which part of a circular bacterial genome is least conserved?
• Aside strand bias: (G/G+C) other biases.

If time sequence space, Ebola?