PhyloVerse Documentation

Getting Started

PhyloVerse runs entirely in your browser with no installation required. The new split-pane interface lets you see your tree visualizations update in real-time as you adjust settings.

Interface Overview

PhyloVerse uses a three-panel layout inspired by professional phylogenetics software like iTOL. Each panel serves a specific purpose.

Left Sidebar Sections

• Upload: Drag and drop files or click to browse
• Samples: Load curated demo datasets (Dinosauria, Primates, etc.)
• Search: Query GBIF, iNaturalist, eBird for occurrence records
• Data: View loaded specimens with filtering options

Right Sidebar Tabs

• Basic: Tree layout, branch lengths, labels, colors
• Advanced: Bootstrap, Bremer, DEC analysis, tree search
• Datasets: Manage loaded data, apply matrix filters
• Export: SVG, PNG, Newick, NEXUS, CSV exports

Data Upload

PhyloVerse uses intelligent column detection for CSV and XLSX files. If your columns have custom names, the Column Mapper helps you match them to standard fields.

Recognized Column Names

Sample Datasets

Explore PhyloVerse features with 5 real-world datasets. Each includes a phylogenetic tree, geographic specimen data, and morphological character matrix.

Tree Viewer

Interactive D3.js phylograms with full control over tree topology and appearance. The tree updates in real-time as you adjust settings in the right sidebar.

Features

Map Visualization

Leaflet-based maps with markers, heatmaps, flow lines, and range polygons. 3D globe visualization powered by Three.js.

Map Features

Basic Controls

The Basic tab in the right sidebar contains commonly-used visualization settings.

Tree Settings

• Layout: Rectangular, Radial, Circular, Fan
• Branch Lengths: Show/hide proportional branch lengths
• Ladderize: Sort branches by descendant count
• Node Labels: Show taxa names, support values, or both

Style Settings

• Branch Width: Line thickness (1-5px)
• Node Size: Circle radius (2-10px)
• Font Size: Label text size (8-16px)
• Color Scheme: Default, by clade, by trait

Keyboard Shortcuts

Press ? in the app to display all shortcuts.

Biodiversity Integration

Access over 3 billion occurrence records from global biodiversity databases. Use the Search section in the left sidebar to import verified, research-grade observations.

iNaturalist

Community observations with photos, quality grades, and observer information. Over 100 million research-grade observations available.

Quality Levels

eBird

Expert-verified bird observations with counts, dates, and locations. Access to 800+ million bird sightings from around the world.

Setup

GBIF

Global Biodiversity Information Facility with 2+ billion records from museums, herbaria, and field observations worldwide.

Data Sources

• Museum Specimens: Physical vouchers with catalog numbers
• Institutional Data: Expert-identified collections
• Dataset Import: Import entire datasets by UUID

Phylogenetic Analysis

Professional-grade cladistic analysis available in the Advanced tab. All results display inline below each function for easy review. All computations run in your browser.

Support Analysis

• Bootstrap: Character resampling with configurable replicates (10-1000). Shows support values directly on tree nodes with average support and strong node count.
• Bremer Support: Calculate decay indices for each node. Higher values indicate more robust clades.
• Jackknife: Delete-percentage character resampling (configurable 10-50%).
• Bayesian Posterior: MCMC-based posterior probability estimation with ESS tracking.

Tree Search

• Parsimony Ratchet: Escape local optima with iterative perturbation. Progress bar shows current best length.
• Branch Swapping: TBR (most thorough), SPR (balanced), or NNI (fastest) tree rearrangement algorithms.
• Consensus Tree: Build strict consensus, majority-rule (50%), or Adams consensus from multiple trees.

Tree Statistics

Calculate tree length, Consistency Index (CI), Retention Index (RI), and Rescaled Consistency (RC) for your tree and matrix.

Biogeography

Reconstruct ancestral ranges and infer biogeographic events with multiple models.

DEC Analysis

Dispersal-Extinction-Cladogenesis model for ancestral range estimation.

• Configure maximum areas (2-10)
• Estimates dispersal rate (d) and extinction rate (e)
• Reports log-likelihood and event counts
• Reconstructs ancestral ranges on all internal nodes

DEC+J Model

Extended DEC with jump dispersal parameter (founder-event speciation). Compares AIC between DEC and DEC+J to test for jump dispersal significance.

Event Detection

Identify dispersal, vicariance, extinction, and sympatry events across the phylogeny.

Ancestral Area Reconstruction

• Fitch Parsimony: Simple parsimony-based reconstruction
• S-DIVA: Statistical dispersal-vicariance analysis
• BBM: Bayesian Binary Model for probabilistic reconstruction

Character Analysis

Trace character evolution and identify synapomorphies with multiple optimization methods.

Character Tracing

• Select any character from your matrix
• ACCTRAN: Accelerated transformation (favor early changes)
• DELTRAN: Delayed transformation (favor late changes)
• Reports gains (0→1) and losses (1→0) across the tree

Synapomorphy Detection

Generate complete list of shared derived characters for each clade. Results show in a table with character number, name, and state change.

Homoplasy Detection

Identify convergences, reversals, and parallelisms. Reports Homoplasy Index (HI) for data quality assessment.

Character Optimization

• Implied Weights: Downweight homoplastic characters using concavity constant (K)
• Successive Weighting: Iteratively reweight characters by their fit

Molecular Clock & Dating

Date your phylogeny with fossil calibrations and molecular clock models.

Date Calibration

Add fossil or biogeographic calibration points interactively. Each calibration specifies a minimum/maximum age for a node.

• Click "Add Calibration" to define a new calibration point
• Select the node (common ancestor of two taxa)
• Enter minimum and/or maximum age in millions of years (Ma)
• Add multiple calibrations for better precision

Molecular Clock Models

• Strict Clock: Constant substitution rate across the entire tree
• Relaxed (Lognormal): Rates vary and are drawn from a lognormal distribution
• Relaxed (Exponential): Rates vary and are drawn from an exponential distribution
• Local Clocks: Different rates for specified clades (useful for rate heterogeneity)

Divergence Time Estimation

Estimate node ages with 95% Highest Posterior Density (HPD) confidence intervals. Reports:

• Root age with confidence interval
• Average HPD width (narrower = more precise)
• Node-by-node age estimates

Diversification Analysis

Analyze speciation and extinction dynamics across your phylogeny.

Lineages Through Time (LTT)

• Visualize how lineage diversity accumulates over time
• Gamma statistic: Tests for variation in diversification rate (negative = slowdown, positive = acceleration)
• Compare empirical LTT to null models

Birth-Death Models

• Speciation rate (λ): Rate of new lineage origination
• Extinction rate (μ): Rate of lineage loss
• Net diversification (r): λ - μ
• Turnover (ε): μ / λ

BAMM Analysis

Bayesian Analysis of Macroevolutionary Mixtures detects rate shifts across the tree:

• Identify branches where diversification rate changed
• Map rate variation onto the phylogeny
• Test for correlation with traits or biogeographic events

Comparative Methods

Analyze trait evolution while accounting for phylogenetic relationships.

Phylogenetic Signal

• Blomberg's K: Test for phylogenetic clustering of traits (K>1 = conserved, K<1 = convergent)
• Pagel's λ: Estimate phylogenetic signal strength (0 = no signal, 1 = Brownian motion)

Ancestral State Reconstruction

• Maximum Likelihood: ML estimation of continuous ancestral values
• PIC: Phylogenetic Independent Contrasts
• PGLS: Phylogenetic Generalized Least Squares

PGLS Regression

Perform correlation analyses accounting for phylogeny. Reports slope, R², p-value, and estimated λ.

History & Undo/Redo

PhyloVerse tracks all your actions with a full undo/redo system.

Features

• Unlimited Undo: Up to 50 states saved automatically
• History Tab: View and restore any previous state
• Keyboard Shortcuts: Ctrl+Z to undo, Ctrl+Y to redo
• Inline Results: All analysis results display below the function and are saved to history

Restoring States

Click on any item in the History list to restore to that point. All changes made after that point can be recovered using Redo.

Resizable Panels

Customize your workspace by resizing panels to fit your needs.

Sidebar Resizing

• Drag to resize: Hover near the edge of either sidebar until you see the resize cursor
• Drag horizontally: Move the edge to make the panel wider or narrower
• Double-click to reset: Restore the panel to its default width
• Touch support: Works on touch devices as well as desktop

Width Limits

Panels can be resized between 200px and 500px width to ensure content remains readable.

Split View

View your phylogenetic tree and geographic map side by side.

Using Split View

• Click the "Split" tab in the view switcher or press 4
• Tree displays on the left, map displays on the right
• Specimens from your data automatically appear on the map

Resizing the Split

• Drag the divider: Adjust the proportion between tree and map views
• Double-click to reset: Return to 50/50 split
• Touch support: Works on tablets and mobile devices

Export Options

Export trees, maps, data, and project states from the Export tab in the right sidebar.

Data Formats

PhyloVerse supports standard phylogenetic and biodiversity data formats.

Input Formats

• NEXUS (.nex): Tree and character matrix
• Newick (.tre, .nwk): Tree topology with branch lengths
• CSV/XLSX: Specimen occurrence data
• Darwin Core (.tsv): GBIF downloads (up to 50,000 records)
• Hennig86 (.ss): Character state matrices

Citation

If you use PhyloVerse in your research, please cite:

Data Source Citations

iNaturalist

iNaturalist.org. iNaturalist Research-grade Observations. https://doi.org/10.15468/ab3s5x accessed via PhyloVerse on [DATE].

eBird

eBird. 2026. eBird: An online database of bird distribution and abundance. Cornell Lab of Ornithology. http://www.ebird.org (Accessed: [DATE])

GBIF

GBIF.org ([DATE]) GBIF Occurrence Download https://doi.org/10.15468/dl.XXXXX