Add the num_lines( ) function.
Add function Parameters::show_h_tree()
Fix comment.
Don't crash when SPRing to current branch -- do nothing.
Print branch lengths in show_h_tree().
In P::SPR( ), invalidate transition matrices.
Remove special invalidation of transition_P, since SPR handles this now.
Change SPR_at_location( ) to also invalidate transition matrices.
Remove unnecessary invalidations.
Move more invalidation to SPR_at_location( ).
Invalidate the subA indices for branch BM.
Remove need for P.set_tree(T0) in every iteation of SPR_search_...( )
Fix typo.
Improve documentation for alignment utilities.
Mention the sequence name that contains a letter out of the alphabet.
Fix typo.