v0.1.2 (BUGGY – DO NOT USE!)

• Modified Fasta2UShER to use faToVcf resulting in substantial speedups. Bug fixes to Fasta2UShER.
• Modified core data structures in UShER resulting in some speedups.
• Added an experimental option --multiple-placements in UShER to create a new tree for each possibility of parsimony-optimal placement
• Replaced collapse-final-tree with collapse-tree
• Added a note in README about mutation-annotated tree protobuf shared via UCSC for public SARS-CoV-2 sequences

v0.1.1

Major changes:

1. Multi-token command-line options added for brevity
2. Added command-line options to sort new samples based on the number of parsimony-optimal placements and parsimony scores before the actual placement
3. Ubuntu install script now builds with ARM processors

Initial release for the pre-print

v0.1.0

Updated reference