limit block maximum divergence

[mmolari]

• remove tree balancing
• makes accepting block mergers more strict, depending on the alignment divergence.
  • given a proposed merger between two blocks $b_{1,2}$, calculate maximum divergence of the two block alignments $d_{1,2}$
    • this is calculated as the number of substitutions in the alignment, divided by the consensus length minus the total number of deletions. Care is also taken in excluding mutations involving ambiguous nucleotides.
  • the merger comes with its own consensus-alignment divergence $d_A$. The merger is refused if $d_A + d_1 + d_2 > 1 / \beta$.