Add two new builtins, and module Alignment to contain them.
Add new builtin transition_counts.
Add builtin pairwise_alignment_probability_from_counts.
Move alignment_branch_pr to Alignment.hs.
Add filter to Prelude.
Add node predicates and node lists to Tree.
Add some initial stabs at alignment probability code to Alignment.
Move code outside of loop.
Add new functions.
Use new code.
Write 'tree' instead of 't'.
Remove unused code.
Make list of pairwise alignments.
Switch to list of alignments.
Make an array of branch hmms.
Look up things in the hmms array.
Add indices for new alignment probabilities.
Initialize data_partitions after creating MyTree.tree.
Fix alignment_prior_top.
Check that alignment_pr_top gets the right value.