v0.6.3

• Several minor bug fixes (#329 – #355)

v0.6.2

• Minor bug fixes (#317 and #320).

v0.6.1

• Minor bug fixes for Pangolin update #304 – #307

v0.6.0

• Releasing new programs usher-sampled and ripples-fast
• Many bug fixes and feature additions in PRs #251 – #295

v0.5.6

• Added simulation scripts for RIPPLES (#250).

v0.5.5

• Updated RIPPLES workflow (#249).
• Added matOptimize publication details.

v0.5.4

• Keep protobuf generation in sync (#226)
• Radius doubling on the final round of optimization in matOpimize (#223)
• Fix indexing bug that can cause overspecific clade assignment (#234)
• bugfix to metadata reader
• Some additional bugfixes (#229)

v0.5.3

• New -M option in matUtils mask to forcibly move nodes within the tree (#220)
• New -U option in matUtils extract to select ALL samples under the MRCA of the current sample set (#220)
• Codon change string provided in matUtils summary translation output (#220)
• New --closest-relatives option added to matUtils extract (#218)
• New --include-nt option added to matUtils extract --write-taxodium (#216)
• Fixed vcf importer in matOptimize (#208)
• Modified clade assignment logic

v0.5.2

• Faster ripples as ripples-fast (#200 and #202).
• Refactor and clean up of matUtils introduce for the preprint. Whitelist samples that would otherwise be pruned or not included, added to matUtils extract (#198).
• Bug fix in usher for printing parsimony scores using -p flag.

v0.5.1

• Using OpenMPI for matOptimize (#194)
• Using isa-l for file decompression (#192)
• Bugfixes in maatOptimize (#184)
• New taxodium output functionalities (#191)
• matUtils: generic masking of mutations, bugfix to introduce