BPPT - BPP Tree Viewer

A web and desktop application for viewing MCMC trees from BPP (Bayesian Phylogenetics and Phylogeography) analysis.

Features

• View species trees from BPP MCMC output (.mcmc.txt files)
• Embedded gene trees within species tree "tubes" showing coalescent events
• Multiple view modes: Phylogram and Cladogram
• Navigate posterior samples with slider, keyboard, or direct input
• Adjustable dimensions with height and width sliders
• Display theta values (population size parameters) on branches

Web Version

Try it online: https://bpp.github.io/bppt/

Desktop Downloads

Download installers from Releases:

• macOS: .dmg (Intel and Apple Silicon)
• Windows: .exe installer
• Linux: .AppImage

Usage

Loading Species Trees

1. Click "Choose File..." to open a BPP MCMC output file (e.g., mcmc_out.mcmc.txt)
2. The first posterior sample will display automatically
3. Use the slider or arrow keys to navigate through samples

Loading Gene Trees (Optional)

To visualize gene tree coalescences within species tree populations:

1. Load a species tree file first
2. Click "Imap..." to load the individual-to-species mapping file (e.g., imap.txt)
3. Click "Gene Trees..." to load gene tree files (e.g., mcmc_out.gtree.L1, mcmc_out.gtree.L2, etc.)
4. Select locus from the dropdown to switch between loci

View Controls

• View selector: Switch between Phylogram (branch lengths proportional) and Cladogram views
• Show θ checkbox: Toggle display of theta values on branches
• Height slider: Adjust tree height (tips fixed at top, root extends downward)
• Width slider: Adjust tree width (species tubes scale proportionally)

Navigation

• Slider: Drag to jump to any posterior sample
• ◀ / ▶ buttons: Previous/next sample
• Arrow keys: Left/Right for previous/next
• Page Up/Down: Jump 100 samples
• Home/End: Jump to first/last sample
• Direct input: Type a sample number and press Enter

Input File Formats

Species Tree File (.mcmc.txt)

BPP MCMC output containing Newick trees with theta annotations:

((A:0.001,B:0.001):0.002,(C:0.001,D:0.001):0.002):0.003 #0.05 [theta values...]

Gene Tree Files (.gtree.L*)

BPP gene tree output with individual labels in Species^individual format:

((A^a1:0.0001,A^a2:0.0001):0.001,(B^b1:0.0002,B^b2:0.0002):0.001):0.002; [TH=0.003]

Imap File

Tab-separated file mapping individuals to species:

a1	A
a2	A
b1	B
b2	B

Building from Source

# Install dependencies
npm install

# Run development server
npm run dev

# Build web version
npm run build

# Build Electron app for current platform
npm run package

License

MIT