On Wed, 13 Oct 2004 06:13:48 +0000 (UTC), SuperNerdGirl{at}gmail.com
(SuperNerdGirl) wrote:

>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

On your first question about gaps, try Googling on "gap penalty" or,
more particularly,"gap insertion extension".

On your third question, try Googling on "long branch attraction".

Can it really be true that you have spent a lot of time exploring
these questions without ever trying to look up the subjects on google?
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