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RaxmlGUI2

A desktop GUI for RAxML.

Development

This is a an Electron App that was bootstrapped with Create React App.

yarn start will start the Electron app and the React app at the same time.
yarn build will build the React app and package it along the Electron app.

End-to-end tests

E2e tests use Playwright to drive the real Electron app against the CRA dev server and the bundled RAxML binaries. Specs in e2e/ load the dev prefilled nucleotide alignment and check the UI and output files:

  • modeltest-then-raxml-ng.spec.js — ModelTest, then a full raxml-ng analysis
  • raxmlHPC.spec.js — classic raxmlHPC (ML search)

Download binaries once, then run:

yarn download-binaries
yarn test:e2e

The test harness sets RAXMLGUI_E2E=1 when launching Electron. That disables DevTools and auto-update checks, and points the main process at the repo static/ directory (example files, binaries, and test output) instead of the packaged app resources path.

Input formats

RaxmlGUI supports both FASTA and PHYLIP format.

The strict phylip format reserves the first ten characters before each sequence for the name. The relaxed format allows longer name but requires no space within the name to know where it ends.

Examples

Phylip interleaved strict

      5    42
Turkey    AAGCTNGGGC ATTTCAGGGT
Salmo gairAAGCCTTGGC AGTGCAGGGT
H. SapiensACCGGTTGGC CGTTCAGGGT
Chimp     AAACCCTTGC CGTTACGCTT
Gorilla   AAACCCTTGC CGGTACGCTT

GAGCCCGGGC AATACAGGGT AT
GAGCCGTGGC CGGGCACGGT AT
ACAGGTTGGC CGTTCAGGGT AA
AAACCGAGGC CGGGACACTC AT
AAACCATTGC CGGTACGCTT AA

Phylip interleaved relaxed

      5    42
Turkey     AAGCTNGGGC ATTTCAGGGT
Salmo_gair AAGCCTTGGC AGTGCAGGGT
H._Sapiens ACCGGTTGGC CGTTCAGGGT
Chimp      AAACCCTTGC CGTTACGCTT
Gorilla    AAACCCTTGC CGGTACGCTT

GAGCCCGGGC AATACAGGGT AT
GAGCCGTGGC CGGGCACGGT AT
ACAGGTTGGC CGTTCAGGGT AA
AAACCGAGGC CGGGACACTC AT
AAACCATTGC CGGTACGCTT AA

Phylip sequential strict

  5    42
Turkey    AAGCTNGGGC ATTTCAGGGT
GAGCCCGGGC AATACAGGGT AT
Salmo gairAAGCCTTGGC AGTGCAGGGT
GAGCCGTGGC CGGGCACGGT AT
H. SapiensACCGGTTGGC CGTTCAGGGT
ACAGGTTGGC CGTTCAGGGT AA
Chimp     AAACCCTTGC CGTTACGCTT
AAACCGAGGC CGGGACACTC AT
Gorilla   AAACCCTTGC CGGTACGCTT
AAACCATTGC CGGTACGCTT AA

Phylip sequential relaxed

  5    42
Turkey     AAGCTNGGGC ATTTCAGGGT
GAGCCCGGGC AATACAGGGT AT
Salmo_gair AAGCCTTGGC AGTGCAGGGT
GAGCCGTGGC CGGGCACGGT AT
H._Sapiens ACCGGTTGGC CGTTCAGGGT
ACAGGTTGGC CGTTCAGGGT AA
Chimp      AAACCCTTGC CGTTACGCTT
AAACCGAGGC CGGGACACTC AT
Gorilla    AAACCCTTGC CGGTACGCTT
AAACCATTGC CGGTACGCTT AA

MacOS code-signing and notarizing

https://medium.com/@TwitterArchiveEraser/notarize-electron-apps-7a5f988406db https://github.com/electron/electron-notarize https://stackoverflow.com/questions/53112078/how-to-upload-dmg-file-for-notarization-in-xcode/53121755#53121755

Publishing with electron-builder

Need to have a GH_TOKEN in your shell env

Binaries

The binaries for RAxML on MacOS were compiled from this repository: https://github.com/jtklein/standard-RAxML