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Change History

tact 0.4.1

  • Extreme age ranges when using the Yule or birth-death models should now cause fewer optimization issues (reported by Alexandre Siqueira).

tact 0.4.0

  • Drops support for Python 3.6.
  • tact_add_taxa gains --ultrametricity-precision to control the precision of ultrametricity checks (reported by Miao Sun, #230).

tact 0.3.4

  • Introduces a new dual-optimizer algorithm, which uses simulated annealing to estimate diversification rates when the standard optimizer fails. This should address optimization problems that occur when estimating parameters on particularly species-rich or species-poor groups.
  • Rate estimation is now optimized for cherries (by not estimating them at all).
  • Improved reporting of which species in the backbone are breaking desired taxonomic monophyly.
  • Full support for Python 3.9.

tact 0.3.3

  • TACT now uses DendroPy 4.5.1.

tact 0.3.2

  • Fixes a numerical precision issue in certain phylogenies with zero length branches (reported by Marcio Pie).
  • Logs now have a more standardized format.

tact 0.3.1

tact 0.3.0

  • tact_build_taxonomic_tree now sorts its input on the user's behalf (suggested by Marcio Pie).
  • tact_build_taxonomic_tree automatically generates unique rank names.
  • tact_build_taxonomic_tree detects and warns on empty input cells.
  • tact_build_taxonomic_tree checks that the phylogeny it produces is valid.
  • tact_add_taxa now has fewer annoying warnings.

tact 0.2.7

  • Fixes some DendroPy messages in tact_add_taxa that were erroneously passed to the user.

tact 0.2.6

  • Internal automation improvements.

tact 0.2.5

  • Fixes a rare optimization bug when using the Yule model
  • Fixes a rare optimization bug when analysing particularly small phylogenies.

tact 0.2.4

  • Internal automation improvements.

tact 0.2.3

  • tact_add_taxa now correctly restores terminal settings when quitting (reported by Joseph W. Brown, #101).
  • tact_add_taxa now assumes in more places that its input trees are rooted.

tact 0.2.2

tact 0.2.1

  • Updates to TACT's unit tests and dependencies.

tact 0.2.0

  • tact_add_taxa gains a --yule option for pure-birth rate estimation.
  • Fall back to arbitrary-precision math in more circumstances.

tact 0.1.4

  • Update NumPy dependency to 1.17.

tact 0.1.3

  • Migrate to Poetry build system
  • Remove poor-performing parallel MRCA rate calculation algorithm

tact 0.1.2

  • Adds example taxonomy and backbone files to the distribution.
  • This is the version that was reviewed for Chang et al. (2019).

tact 0.1.1

  • Fixes a phylogeny generation bug in tact_build_taxonomic_tree.

tact 0.1.0


Last update: October 11, 2021