Python value comparing taking too long
One observation is that you are converting the splitted[1] to float inside the inner loop - redoing the same exact thing multiple times - do it once before the loop:

splitted = float(read.split(" ", 1)[1])  # convert to float here
for k in range(i + 1, num_lines + 1):        
    read1 = linecache.getline('just_nodes.txt', k).rstrip('\n')
    splitted1 = float(read1.split(" ", 1)[1])

    alpha_temp = abs(splitted - splitted1)


Note the other thing I've done - splitting by an explicit space and doing it strictly once - please check if it actually has a positive impact on performance.

You may also not strip the newlines from the end of the lines, float() can handle it:

In [1]: float("1.00\n")
Out[1]: 1.0