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

v0.3.5

• --clade-paths option for matUtils annotate
• Manual version tagging

v0.3.4

Fixing version issues.

v0.3.3

• Faster rsearch
• RoHo functionaility in matUtils summary
• Attempt to fix version number for bioconda/release folders

v0.3.2

• Faster usher placement by avoiding computing mutation vectors except for best nodes.
• Updates to matUtils introduce for printing cluster-level statistics and sorting the output by relative order of priority for attention.
• Bugfixes to matUtils extract -z and matUtils extract -X.
• New matUtils extract selection option (-I) which gets samples descended from a specified internal node.
• Added matUtils reference to the README.

v0.3.1

• New options for Pangolin clade assignments.
• New metadata in matUtils extract.
• Option to make install.

v0.3.0

• Improved heuristic to matUtils annotate
• Faster, improved matOptimize. Takes in a VCF between multiple iteration to do full Fitch-Sankoff.
• Include the histogram of clade assignments for multiple equally parsimonious placements.
• Addition of matUtils introduce command for phylogeographic analysis and statistics.
• Addition of support for the writing/reading of Augur JSON files to matUtils extract.
• Parallel JSON extraction.
• Numerous bugfixes, minor behavioral changes, and new options for matUtils extract, uncertainty, and summary.
• Added matUtils mask --simplify option to identify sets of condensable leaves and remove all but one leaf from each set.
• Added version numbers.

v0.2.1

• Faster and parallel uncondense_leaves.
• A few bug fixes.
• Improved matUtils annotate and matOptimize algorithms.

v0.2.0

Major changes:

• Introducing matUtilsutility with the following functionality
  • summary provides a summary information for an input MAT, such as the number of nodes, leaves, parsimony score, clades etc.
  • extract takes an input MAT and can extract a subset (such as a mutation-annotated subtree of user-specified input samples) and produces an output MAT, Newick tree, VCF or JSON. It also contains a long list of commands to extract other useful information from a MAT such as mutation paths for a set of samples.
  • annotate can be used to annotate internal nodes of an input MAT with clade names
  • uncertaintycan be used to calculate uncertainty metrics, such as the number of equally parsimonious placements for a given sample
• Introducing a preliminary version of matOptimize that can be used to optimize the parsimony score of an input MAT using tree moves
• Protobuf format changed to accommodate the above two changes. matToVcf function has been moved to matUtils extract
• Fasta2UShER has been replaced by a set of bash commands
• Several performance optimizations

v0.1.4

• Added conda installation instructions
• Added matUtils to handle masking of mutations
• Implemented a few performance optimizations (faster uncondense, dfs traversal etc.)
• Modified save --save-mutation-annotated-tree to always condense the tree before saving
• Modified the Dockerfile to checkout the latest release version before build