It's VERY inefficient to open/read/close the same file three times, not to mention it just makes for more work to address multiple variables with sequentially-number names. The existence of such is a very good sign that MATLAB syntax isn't being used effectively.
Instead, do something more like
data=readmatrix('phasesintegrated'); % read the whole array at once
plot(data(:,1),data(:,2),'b-','linewidth',2);
hold on % so can add to same axes
plot(data(:,1),data(:,3), 'bo-','linewidth',1);
Not sure what else, specifically you want to plot, but the "every fifth point" thing is trivial -- see <colon, :> for all the skinny on subscripting, but
nSkip=5;
plot(data(1:nSkip:end,1),data(1:nSkip:end,2),'rx');
would add the 2nd set of data with a red 'x' for every fifth point beginning with the first. You can change the starting index at will, too, of course.
