Use the command Seq hominoids=Seq primates([1:5],:) to extract the sequences for the hominoids. Some of the sequences have gaps, indicated by the “–” character. Sites where any sequence has a gap...

to extract the sequences for the hominoids. Some of the sequences have gaps, indicated by the “–” character. Sites where any sequence has a gap should be removed before computing distances. The commands

gaps=(Seq hominoids =='-')

gapsites=find(sum(gaps))

Seq nogaps=Seq hominoids

Seq nogaps(:,gapsites)=[ ]

will find and delete those sites. Using the gapless sequences, compute the Jukes-Cantor, Kimura 2-parameter, and log-det distances. Recall that [DJC, DK2, DLD]=distances(Seq nogaps) will do this easily.

a. How similar are these distances to those in the array Dist primates?

b. Use each distance array you produce to construct a tree by Neighbor Joining. Are they all the same topologically? Metrically?