Move get_bitpath_3way into A3::get_bitpath( ).
Create sample-two-nodes2.C and use it.
Simplify loop.
Refactor code for allowed states.
More simplification.
Replace {i,j,k,l}col with a bitpath.
Eliminate cached_dparrays.
Use an HMM to create the DParray.
Remove constructors for DP objects that don't take an HMM.
Pass in original tree and alignment.
Add A5::get_bitpath( ).
Use a1234 instead of seqall to get the array length.
Construct the a1234 order matrix from P0 and nodes0.
Mark the hidden bits on the HMM.
Compute the masks from the HMM.
Clean up computation of allowed states in sample-node.C.
Use the new method of constructing alignments!
Remove the old way of setting the alignment.
Remove comment.
Remove hidden bits as well as empty columns.