Source: https://github.com/MurrellGroup/swig
Inspected revision: 874c32fadb97b36ace6d3df98839cfec1bda0799.
Copyright (c) 2026 MurrellGroup. MIT license, retained in public/vendor/SWIG-LICENSE.txt.
public/core.js adapts the undirected graph/orientation approach of SWIG's src/phylogeny.ts for rerooting, with generic midpoint edge splitting and edge-associated internal support. SWIG's linked tree/alignment view and exact numeric-label FastTree input conventions informed this app. The rest of the interface and implementation were written for this workbench. No SWIG IMGT or other biological reference data are bundled.
FastTree 2.1.11, by Morgan N. Price and contributors.
Copyright (C) 2008–2015 The Regents of the University of California.
Source license: GPL version 2 or, at your option, any later version. This distribution uses GPLv3; the complete license is in LICENSE and public/vendor/FASTTREE-LICENSE.txt. Corresponding C source, compatible rebuild script and provenance are in public/vendor/.
Upstream: https://github.com/morgannprice/fasttree Documentation: https://morgannprice.github.io/fasttree/
Scientific citation: Price MN, Dehal PS, Arkin AP (2010). FastTree 2—Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE 5(3): e9490. https://doi.org/10.1371/journal.pone.0009490
The unmodified precompiled FastTree module and JavaScript glue are from Biowasm's 2.1.11 CDN package. Biowasm is MIT-licensed; its license is in public/vendor/BIOWASM-LICENSE.txt. Source: https://github.com/biowasm/biowasm . File provenance and SHA-256 hashes are supplied next to the files.
The generated runtime includes Emscripten code. Upstream license is preserved in public/vendor/EMSCRIPTEN-LICENSE.txt. Source: https://github.com/emscripten-core/emscripten . System-library source and individual notices are maintained upstream. The FastTree source header retains additional acknowledgements and notices for incorporated scientific routines.
jsdom 26.1.0 and its dependencies are installed by npm only for DOM integration testing. They are not shipped to or loaded by the production app. Their precise versions and license identifiers are retained in package-lock.json; npm packages carry their own license files.
EvoOnline source: https://github.com/MurrellGroup/EvoOnline . Inspected revision: 9de144b5d4cf682ab3402f31d5dd4deee33cb638. Copyright (c) 2026 Murrell Group contributors, MIT; complete notice retained in public/vendor/EVOONLINE-LICENSE.txt.
The compact Mol* viewer options, MolViewSpec scene construction, residue color layers, grouped molecular surfaces, camera retention, and per-chain Show/Map/cartoon/atoms/surface/global-opacity controls are adapted from its apps/web/src/features/structure-mapping/ implementation. Arbor uses the user-supplied HTML's mapping method rather than EvoOnline's profile alignment method.
Mol* 5.11.0 is bundled locally under MIT; see public/vendor/molstar/LICENSE and PROVENANCE.md. Both JavaScript and CSS exactly match the integrity hashes pinned in EvoOnline. The JavaScript retains bundled dependency license notices. Upstream source: https://github.com/molstar/molstar/tree/v5.11.0 .
The attached interfacer.html supplies the amino-acid profile construction and BLOSUM62 affine-gap local-alignment algorithm, adapted into public/structure/profile.js. Its atom-hierarchy chain extraction informed public/structure/viewer.js. The original mapping functions are retained as a test fixture for exact parity checks. The 1BRS PDB file embedded in the attachment is retained only as a test fixture; no interface/contact analysis code or unrelated embedded viewer bundle from that HTML is shipped in the app.
PDB test data: entry 1BRS, originally from the Protein Data Bank. The supplied file retains its original PDB header and attribution records. It is used to test parsing and mapping, not as evidence of a biological comparison; tests create synthetic mutations explicitly.