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

v0.1.3

• Added matToVcf to generate a VCF and/or newick file corresponding to the mutation-annotated tree
• Added a public docker image to the repository
• Added a DensiTree image to the README for multiple-placements
• Bug fixes to the previous release with the following features:
  • 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