Chapter 6 miscellany

[beroe]

Comments on chapter 6:

• Haven't read ahead yet, but will you talk about amino acid models? (Maybe just mention there are comparable sets of models for AAs?)
• The GTR model 11 parameters. Missing the verb.
• so that they can differ from each other. You go straight into how a-f have to add to 6, but a simple example like you do for π (Just something simple like 0.5 means equal probability of transition from X to Y while 0.2 means ...) would really help explain
• In typical use, mu=1 Should that be µ?
• That means that the best possible likelihood under HKY85 is also available under GTR -- good message.
• there are challenges far short of this extreme example - little bit awkward?
• When talking about I and G maybe use the Γ symbol and put (gamma) in parentheses? G is usually a lazy shortcut for finding the gamma key, right?
• the topology we are evaluating is the focal topology -- should be as the -- and maybe bold focal topology.
• focal tree as a whole be asking how frequent -- by asking
• It jsut indicates how frequently an edge is recovered--> just

[caseywdunn]

Will get to amino acids later. Decided to focus entirely on DNA while putting all the pieces together, then circle back and add other approaches in.