Fix typo.
Allow accessing the dp_order vector directly.
Add T0 argument to tri_sample_alignment_base2( )

Allow checking if the tree has changed by passing in the original tree.
Pass in p[0][j] so that we have access to the original alignment.
Create new alignment from pairwise alignments!

Stop using A3::construct( )!
Eliminate now-unused seq2 and seq3 vectors.
Remove some debugging cruft.

Hopefully this is no longer needed.
Rename columns to seq123.
Remove need for seq12 when pinning alignments.
Actually rewrite get_pins( ) to work without the sequence order.
Construct the HMM that we will use.
Reorder construction of seq1, seq12, and seq123.
Add A3::get_nodes_branch( ).
Move more code into sample-tri2.C
Don't destroy pairwise alignments if the tree didn't change.
Define seq1 in a different way.
Improve construction of a23.
Add function get_column_order( ).
Use get_column_order( ) to construct seq23_ and seq123_
Use newly constructed column orders.