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BRANCHSNV v0.1.0

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@RhysWhite RhysWhite released this 13 Aug 13:00
v0.1.0
a17c252

First stable release of BRANCHSNV, a dependency-free Python command-line tool for separating strict clade-exclusive nucleotide markers from reconstructed focal-edge substitutions in rooted phylogenies.

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BRANCHSNV v0.1.0a1

BRANCHSNV v0.1.0a1 Pre-release
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@RhysWhite RhysWhite released this 31 Jul 02:31
v0.1.0a1
aeca84f
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BRANCHSNV v0.1.0a1

This is the first alpha release of BRANCHSNV, a dependency-free Python
command-line tool for reproducible identification of branch-associated
single-nucleotide variants from rooted phylogenies and transposed NEXUS
matrices.

Included functionality

  • strict parsing of transposed nucleotide NEXUS matrices;
  • strict parsing and explicit rooting of Newick phylogenies;
  • exact matching of tree tips and alignment taxa;
  • branch selection by exact descendant membership, MRCA, or deterministic
    branch identifier;
  • identification of fixed-exclusive clade markers;
  • equal-cost Sankoff maximum-parsimony reconstruction across a selected branch;
  • explicit handling of missing and ambiguous nucleotide states;
  • deterministic TSV, branch-membership, and JSON provenance outputs;
  • SHA-256 recording of inputs and outputs;
  • no runtime dependencies.

Validation

  • 42 automated tests;
  • Python 3.10–3.14 testing on Ubuntu;
  • Python 3.14 testing on macOS and Windows;
  • byte-identical bundled-example reproduction across operating systems;
  • wheel and source-distribution metadata validation;
  • independent installation and validation of both distribution formats;
  • confirmation that no runtime dependencies are declared;
  • verified SHA-256 checksums for all attached release files.

Alpha status

This release is intended for testing and review.

The real-data AK3 validation reproduces the published MRSA AK3 branch SNV
coordinates. An unresolved discrepancy remains between the supplied working
inputs and the published SaPITokyo12571-like branch table. This discrepancy is
documented as an open release-blocking issue and must be resolved before the
stable v0.1.0 release.

BRANCHSNV does not currently reconstruct insertions, deletions, structural
variants, or recombination events.

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