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