https://github.com/broadinstitute/delphy - 1.0.3

• Ignore spaces in FASTA IDs (to align with BEAST & IQ-Tree)
• Fix Emscripten compilation glitches

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Published by patvarilly about 1 year ago

https://github.com/broadinstitute/delphy - 1.0.2

• Tweak Colab tutorials (#4)
• Allow for clean compilation in Ubuntu 22.04 AWS instance

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 1.0.1

• Add Colab tutorials (#3)
• Add option to embed web-UI metadata in .dphy files from CLI

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 1.0

• Final tweaks to tip-date sampling before preprint

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.999932

• Fix flatbuffer corruption when site-rate heterogeneity enabled (Issue #35 on delphy-web)
• Misc internal fixes

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.999931

• Critical bugfixes for tip date sampling

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.99993

• Add support for uncertain tip dates ("tip-date sampling")
• Revive innernodedisplace_move() that was effectively turned off by mistake
• Port delphy_ui to SDL2 (remove dependency on OpenGL/GLUT to ease compilation on Mac)

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.99992

• Core changes to support better progress, warning and error reporting in web UI

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.99991

• Defend against underflow issues when site-rate heterogeneity becomes extreme (thanks to David Pascall at the Cambridge Infectious Diseases centre for reporting and helping debug this issue)

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.9999

• WASM improvements:
  • Start memory size very small and grow dynamically as needed
  • Fix communication of 64-bit integers across WASM/JS interface

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.9998

Update dependency management and dependencies

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - 0.9997

• Simplify inner workings of SPR move
• Expose MAPLE input file support in WASM bindings (to support it in web frontend)

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - v0.9996

Minor changes

• Add CLI flags, UI keys and WASM bindings to fix and specify population size and growth rate. Useful for running with constant-size models.
• Add incipient support for Docker (to run in Terra). Thanks, @tomkinsc !
• Make delphy_mcc slightly more general, for use in large-scale benchmarks

- C++
Published by patvarilly over 1 year ago

https://github.com/broadinstitute/delphy - v0.9995

Major changes: * Fix correctness issues with large-scale parallelization

Minor changes: * Add a CLI flag to select number of parallelizable coalescent cells (very large-scale runs need more than the default ~400) * Add an option in the UI to output a FASTA for the current tree, with all missing data resolved (no evolution is simulated between missations and downstream tips); useful for deriving from real datasets a test input file with no missing data * If --v0-seed is specified, different invocations will start with the same initial heuristic tree

- C++
Published by patvarilly almost 2 years ago

https://github.com/broadinstitute/delphy - v0.996

Fix a rare, subtle bug with root-changing mdSPR moves

- C++
Published by patvarilly almost 2 years ago

https://github.com/broadinstitute/delphy - Release mpox adaptations

- C++
Published by patvarilly about 2 years ago

https://github.com/broadinstitute/delphy - Initial public release

- C++
Published by patvarilly about 2 years ago