v4.3.0

What's Changed

• Add filtering by reversions to naive sequence, generalize ranking strategy by @willdumm in #130
  • adds new --ranking_strategy argument, which takes a string consisting of a comma-separated list or linear combination of ranking criterion identifiers.
  • deprecates inference arguments --branching_process_ranking_coeff, --ranking_coeffs, and --use_old_mut_parsimony in favor of the new --ranking_strategy argument. These old options will still work but will throw warnings.
  • adds counts of reversions to the naive sequence as a new ranking criterion
  • adds --show_nucleotide_mutations argument, to specify that rendered tree should have nt mut annotations.
  • modifies all ranking criteria so that smaller values are better. Log likelihoods are negated, and referred to as log loss.

Full Changelog: v4.2.2...v4.3.0