Release Notes

Version 1.1.0: Sept. 16, 2019

  • Added parsimony reconstruction methods for cell subsets. Information for Austin, Buckner et al. (2019) hardcoded. More general methods and documentation to follow.

Version 1.0.7: Feb. 19, 2019

  • Added HLP19 substitution model, specified by HLP or HLP19.
  • Constant B matrix approximation (–cbmat; default for HLP) dramatically improves runtime.
  • Default for –motifs is now FCH (free coldspots and hotspots).
  • FWR/CDR omega optimization is default behavior if partition files included.
  • Output file cleaned up, as well as confidence interval prediction output.

Version 1.0.6

  • Repertoire-wide HLP17 parameter optimization
  • Parallelization by tree using –threads
  • Integration to Change-O through BuildTrees.py