Build Spatial Phylogenies Fast with GeoPhyloBuilder

Visualize Evolution Across Landscapes — GeoPhyloBuilder Guide

Overview

GeoPhyloBuilder is a tool for integrating phylogenetic trees with geographic data to create interactive visualizations that show evolutionary relationships across space. This guide explains core features, typical workflows, and best practices for producing clear, publication-quality geo-phylogenetic maps.

Key features

• Tree–map integration: Overlay phylogenetic trees on geographic maps so clades and branches correspond to spatial locations.
• Time-aware visualization: Animate lineage movements through time using dated trees or inferred ancestral states.
• Ancestral state inference: Reconstruct likely ancestral locations and display uncertainty (e.g., heatmaps or confidence ellipses).
• Custom styling: Color branches by trait, clade, or geographic region; adjust branch thickness, node size, and labels.
• Interactive export: Export web-ready interactive maps (GeoJSON/Leaflet/Deck.gl) and static high-resolution figures for publication.
• Batch processing: Process multiple trees or large datasets via command-line tools or APIs.

Typical workflow

1. Prepare inputs
   • Phylogenetic tree in Newick or Nexus (dated preferred for time animation).
   • Sample metadata with coordinates (latitude, longitude), sample IDs matching tree tips, and optional traits.
2. Preprocess
   • Clean metadata, ensure tip names match tree labels, convert coordinates to consistent CRS (WGS84).
   • If trees lack dates, optionally time-calibrate or use relative branch lengths.
3. Infer ancestral locations (optional)
   • Use built-in models (parsimony, likelihood, Bayesian) or import results from external tools.
4. Map rendering
   • Choose base map (satellite, terrain, plain).
   • Overlay branches as great-circle arcs or straight lines; display nodes with size/color encoding.
   • Add legends, scale bars, and annotations.
5. Animate & interact
   • Create time sliders, play/pause controls, and hover tooltips showing metadata.
6. Export
   • Save interactive HTML or static PNG/SVG with publication settings.

Best practices

• Match tip labels exactly between tree and metadata to avoid missing tips.
• Project coordinates to WGS84 for web maps; reproject for regional maps if needed.
• Simplify dense trees by collapsing poorly supported clades or subsampling to improve readability.
• Show uncertainty for inferred ancestral states (e.g., pie charts or confidence ellipses).
• Optimize for performance: convert large trees to simplified geometries or use server-side tiling for very large datasets.

Common use cases

• Tracking pathogen spread over time and space.
• Studying biogeographic history and dispersal routes.
• Visualizing population structure and migration corridors.
• Teaching evolutionary concepts with spatial context.

Example export options

• Interactive: HTML (Leaflet/Deck.gl), GeoJSON layers, embedded JavaScript.
• Static: High-res PNG, SVG for figures, PDF for print.

If you want, I can:

• produce a short step-by-step command-line example for GeoPhyloBuilder using Newick + CSV, or
• create a publication-ready figure checklist tailored to your dataset.