In some ways your question is strange because the solution is to use an array of functions handles instead of an array of function names. You're already using function handles for your problems (whatever these are) which is a bit unexpected. I would have thought that problems would be variables not functions.
alg = {@alg1, @alg2, @alg3}; %array of function handles
for i = 1:numel(alg)
for i = 1:numel(prob)
[M, jM] = alg{i}(prob{j}); %obviously you'd want to store the results in arrays/or cell arrays instead of overwriting them at each step of the loop
end
end
