v0.5.0

• matOptimize uses Intel MPI for parallelization (#180)
• Fixed manual stop and tree drifting in matOptimize (#169 and #180)
• New matUtils output in summary and bug fixes (#170)
• New subtree selection options matUtils(#177)
• Handle multiple metadata files in matUtils taxodium export (#172)
• New usher output file placement_stats.tsv (#176)
• Added option --clade-mutations (-M) for specifying clades by sets of mutations in matUtils annotate (#183)
• Improved snakemake workflows (https://github.com/yatisht/usher/tree/master/workflows)

v0.4.8

• improved memory efficiency in json extraction (#167)
• Changed Dockerfile to use ubuntu 18.04

v0.4.7

• [EXPERIMENTAL] introducing matUtils merge to parallelize UShER placements over multiple worker nodes.
• Faster matOptimize with a higher default for minimum improvement per round (#153)
• More output options in matUtils extract and matUtils summary (#165)
• Improved algorithms and additional output options in matUtils introduce (#162)
• Option to compile usher in server mode (#160).

v0.4.6

• Fixed a bug introduced in the previous release related to uncondensing trees. Thanks to Galya Klink for helping us identify the bug.

v0.4.5 (BUGGY – DO NOT USE!)

• Fixed a bug related to uncondensing leaves.
• New options to specify title and description fields for Taxodium protobof output.
• Workflows updated for taxodium and translate outputs.
• Experimental S and E options in ripples for parallelizing.

v0.4.4

• Don't use native compiler flags, as it could break on non-local (conda) builds.
• Fixed handling of fixed radius in matOptimize.

v0.4.3

• Improvements to search space and a bug fix in matOptimize
• Logging of applied profitable moves in matOptimize

v0.4.2

• matUtils extract includes --write-taxodium option to output taxodium-compatible protobuf files viewable on the web browser.
• Improvements to matUtils introduce.
• New masking routine which performs local or global masking of mutations
• ARM support in matOptimize with a new tree drifting option.
• A few more bug fixes and directory structure cleanup.
• Fixed the logic of getting the nearest subtree.

v0.4.1

• matUtils summary --translate uses UCSC GTF format and handles corner cases.
• New snakemake workflows for usher, matUtils and ripples.

v0.4.0

• Introducing ripples
  • searches for possible recombinant nodes in a MAT using a phylogenetic approach
  • option to limit search to user-specified samples and their ancestors.
• New matOptimize
  • Handles ambiguities and stores Fitch states at each node
  • Faster and better parallelism
  • Exhaustive SPR search
• Several features added to matUtils
  • summary includes a new option --haplotype to collects the number of unique sets of mutations across the entire input tree
  • summary --clades refactored to produces both inclusive and exclusive sample counts
  • summary adds -E option to include contextual information including timespan parsing in RoHO
  • uncertainty includes a new option for identifying locally recurrent mutations
  • new items included in summary --aberrant
  • matUtils annotate includes a new option --clade-paths
• Several changes to improve code quality, including stylizing with ASytle