A next-generation, browser-based platform for phylogenetic analysis, systematics, and evolutionary biogeography. No installation required — 100% in your browser.
The easiest way to load your project is to put all your files in a single folder and drag the entire folder onto the upload zone. PhyloVerse will automatically detect and parse all supported files:
.nex — NEXUS (tree + matrix).tre / .nwk — Newick trees.csv / .xlsx — Occurrence/specimen data.tsv / .txt — Darwin Core Archive (GBIF downloads)NEW.ss — Hennig86 matricesYou can also upload individual files by clicking the upload zone or dragging single files.
Organizing your project files in a folder (e.g., MyProject/tree.tre, MyProject/specimens.csv, MyProject/matrix.nex) makes it easy to reload your entire project at once. Just drag the folder!
Choose from 5 real-world datasets using the dropdown selector, then click "Load Sample". Options include Dinosauria, Primates, Cetaceans, Corvids, and Wild Cats — each with phylogenetic trees, geographic data, and morphological matrices.
The workflow progress bar guides you: Upload → Audit → Visualize → Analyze → Export
PhyloVerse uses intelligent column detection for CSV/XLSX files. If your columns have custom names, the Column Mapper will help you match them.
PhyloVerse recognizes many common column names automatically:
| Field | Recognized Names | Required? |
|---|---|---|
| Taxon/Species | taxon, species, species_, name, scientificName, organism |
Yes |
| Latitude | latitude, lat, decimalLatitude, y, north, lat_dd |
Yes (for mapping) |
| Longitude | longitude, lon, lng, long, decimalLongitude, x, east |
Yes (for mapping) |
| Locality | locality, location, site, place, country, region |
Optional |
| Age (MYA) | age_mya, age, mya, min_age, max_age, period |
Optional |
| Elevation | elevation, altitude, elev, alt, height, elevation_m |
Optional |
| Environment | environment, habitat, biome, ecosystem |
Optional |
If your CSV has non-standard column names (e.g., my_species_name, GPS_lat), the Column Mapper modal will open automatically. Simply select which of your columns corresponds to each field.
Toggle between dark and light themes with Ctrl+D or the theme button. Your preference is saved.
Full keyboard navigation. Press ? to see all shortcuts. Undo/Redo with Ctrl+Z/Y.
Made a mistake? Undo tree manipulations with Ctrl+Z. History tracks up to 50 states.
View tree and map side-by-side with resizable panes. Toggle with Ctrl+\ or the Split button.
Customize branch colors, node shapes (circle/square/diamond/triangle), label fonts in Settings.
Swipe between panels on mobile/tablet. Pinch to zoom on maps and trees.
TBR, SPR, and NNI algorithms for heuristic tree search. Professional-grade cladistic analysis.
Define monophyly constraints and search for optimal trees that satisfy them.
Iterative character reweighting based on CI/RI until tree stability is achieved.
Fast resampling methods for clade support. Goloboff's symmetric resampling included.
Calibrate your tree with fossil dates. Supports strict and relaxed clock models.
Animate character evolution through time. Watch traits change from root to tips.
DIVA-like analysis inferring dispersal, vicariance, and extinction events.
Color-code specimens by altitude. Export elevation-based distribution maps.
Export maps for specific countries or regions. Individual species distribution PNGs.
Calculate Bremer support by character partition. See which data supports each clade.
Press ? in the app to show this list.
Drag folders or files. Auto-detects NEXUS, Newick, CSV, XLSX, Hennig86 formats.
D3.js phylogram with support values, node selection, ladderize, rotate, prune, collapse.
Edit character matrices in-browser. Add taxa/characters, export to NEXUS.
Leaflet maps with markers, heatmaps, flow lines, range polygons, lasso selection.
Three.js globe for global biogeography with time-based filtering.
Fuzzy-match taxa across sources. Flags conflicts, orphans, outliers.
Calculate CI, RI, RC, tree length for parsimony analysis.
List character changes per clade. Export to CSV.
Decay indices for each clade.
Character resampling for clade support.
ACCTRAN/DELTRAN optimization with color-coded branches.
Goloboff's k-value weighting for homoplasy.
Dispersal-Extinction-Cladogenesis for ancestral ranges.
Infer dispersal, vicariance, extinction events.
Define custom areas with color coding.
GBIF, iNaturalist with photos, eBird birds — 3B+ records with quality filtering.
| Export Type | Format | Description |
|---|---|---|
| Tree SVG | .svg | Vector graphic of your tree. Publication-ready. |
| Tree PNG | .png | High-resolution raster image (2x scale). |
| Project JSON | .json | Complete project state. Reload later. |
| Audit CSV | .csv | Data audit results with matches, conflicts, outliers. |
| R Script | .R | Template script for further analysis in R. |
| Specimens by CountryNEW | .csv | Geographic summary grouped by country with elevation and occurrence counts. |
| Elevation ProfileNEW | .csv | All specimens with elevation data, sorted by altitude from highest to lowest. |
| Share URL | Link | Generate shareable URL with project state. |
Choose from 5 real-world datasets to explore PhyloVerse features. Each includes a phylogenetic tree, geographic specimen data, and morphological character matrix.
| Dataset | Description | Taxa | Specimens |
|---|---|---|---|
| 🦖 Dinosauria | Mesozoic dinosaurs from fossil localities | 11 species | USA, Mongolia, Germany, Egypt |
| 🦍 Primates | Great apes and Old World monkeys | 11 species | Africa, SE Asia, worldwide |
| 🐋 Cetacea | Whales and dolphins from ocean surveys | 12 species | Global oceans |
| 🐦 Corvidae | Crows, ravens, and jays | 10 species | N. America, Europe, Asia |
| 🐆 Felidae | Wild cats from conservation surveys | 11 species | Africa, Asia, Americas |
PhyloVerse supports data from major biodiversity databases including GBIF, iDigBio, PBDB, and VertNet. Column names are automatically detected.
PhyloVerse now includes enhanced biodiversity integration with photos, quality filtering, and access to over 3+ billion occurrence records from global databases. Import verified, research-grade observations directly into your project.
Global Biodiversity Information Facility — museum specimens, field observations, and verified occurrence data from institutions worldwide.
Community observations with photos (4 sizes), quality grades, observer info, dates, and direct links. Research Grade filtering available.
Expert-verified bird observations with counts, dates, and locations. Requires free API key from ebird.org/api/keygen (instant approval).
Barcode of Life — DNA barcode sequences with specimen data for molecular phylogenetics.
View observation photos before importing. Grid display with taxon names, quality grades, observer credits, and clickable links to original observations on iNaturalist.
Filter verified vs unverified data for research-quality datasets:
Import options: "Import All" (all quality levels) or "⭐ Verified Only" (research-grade only)
iNaturalist filters:
eBird filters:
Import downloaded GBIF Darwin Core Archive files directly:
occurrence.tsv files (up to 50,000 records for performance)scientificName, decimalLatitude, decimalLongitude, locality, etc.Downloaded archives from gbif.org can be uploaded as .tsv or .txt files
1. Go to Upload Panel → scroll to 🌍 Search Biodiversity Databases
2. Enter species name (e.g., Panthera leo, Parus major, Quercus robur)
3. Check databases: ☑ GBIF ☑ iNaturalist (eBird for birds)
4. Click 🔍 Search & Import
5. Review results and choose: Import All or ⭐ Verified Only
Get your free API key (takes 30 seconds):
Example: Photo-documented, research-grade observations
Panthera leo (African lion)If you downloaded GBIF data manually:
dr340.zip)occurrence.tsv or occurrence.txt| Source | Quality Level | When to Use |
|---|---|---|
| iNaturalist — Research Grade | ⭐⭐⭐ HIGH | Scientific publications, range maps, species distribution modeling |
| eBird — Reviewed | ✅ HIGH | Bird studies, migration analysis, conservation research |
| GBIF — Museum | 🏛️ HIGHEST | Gold standard — physical voucher specimens with expert identification |
| iNaturalist — Needs ID | ❓ MEDIUM | Review manually before use, good for preliminary surveys |
| iNaturalist — Casual | ❌ LOW | Exclude from formal analysis (no location, captive animals, etc.) |
Goal: Create verified bird occurrence map for research paper
Steps:
1. Get eBird API key (free)
2. Search: Haliaeetus leucocephalus (Bald Eagle)
3. Check: ☑ eBird only
4. Import: ⭐ Verified Only
5. View on Map panel
6. Export CSV with full metadata
7. Cite eBird in publication
Result: 200+ expert-verified eagle sightings with dates, counts, and locations
Goal: Show photographic evidence across species range
Steps:
1. Search: Panthera leo
2. Check: ☑ iNaturalist
3. Advanced: ⭐ Research Grade + ☑ Photos only
4. View: 📷 Photo Gallery (verify images are correct species)
5. Import: ⭐ Verified Only
6. View on Globe panel
7. Export map image
Result: 50+ photo-verified observations with locations and observer credits
Goal: Get comprehensive species distribution from multiple sources
Steps:
1. Search: Quercus robur (English Oak)
2. Check: ☑ GBIF ☑ iNaturalist ☑ BOLD
3. Import: Import All
4. Use Data Audit to identify conflicts
5. Filter by quality in Data Table
6. Export combined dataset
Result: 500+ observations from museums, community scientists, and DNA databases
Darwin Core File Size Limit: Browser memory limited to 100 MB per file. Large GBIF downloads (e.g., 2.4 GB) cannot be loaded directly — use API search instead (fetches 300 records per search)
eBird API Limits: Free tier allows 100 requests/day (sufficient for most research)
iNaturalist Photos: Check license before reuse (CC-BY, CC-BY-NC, CC0, or All Rights Reserved)
Darwin Core Records: Performance limit of 50,000 records per file — for larger datasets, use multiple API searches
Citation Required: Always cite data sources in publications (citation format in ENHANCED_BIODIVERSITY_FEATURES.md)
Complete technical documentation with API details, configuration options, and troubleshooting guide.
Quick summary of all enhancements with before/after comparisons and testing checklist.
Original guide covering basic integration, Darwin Core format, and data standards.
Packeer, S. (2025). PhyloVerse v1.1: A next-generation web-based platform for phylogenetic analysis and biogeography. Available at https://shafranpackeer.com