I've been studying for an evolution midterm, and understand most of
the concepts, but I still have a few questions.  It would be greatly
appreciated if you could help clear these concerns:

"When aligning two or more homologous or DNA or amino acid sequences,
gaps may be inserted to maximized their similarity.  ordinarily, two
types of gap  costs are specified.  How do they differ in pronciple
and why might one want to specify differnt values for these two types
of cost?"  I talked to some classmates about that one, and we were all
like, "WTF???".

Also:

Why aren't distance-based methods more popular with systematists?

"What is 'long-branch attarction' and how susceptible are the 3 major
methods of phylogenetic reconstruction to it?"

Thanks a bundle to anyone who can help.

---SuperNerdGirl
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