FossTree

Fossil Calibration Annotation for Bayesian Molecular Dating

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FossTree is a tool for working with fossil calibrations on phylogenetic trees. It reads MCMCTree-format Newick trees with calibration annotations, lets you interactively add and edit calibrations through a GUI, generates BEAST2 MRCAPrior XML blocks, and produces publication-quality tree visualizations.

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Features

• Parse Newick trees with all MCMCTree calibration types: B(), L(), U(), G(), SN(), ST(), S2N()
• Auto-detect MCMCTree format files (e.g. header line 16 1 followed by tree)
• Visualize as cladogram (unscaled) or phylogram (branch-length scaled)
• Interact with nodes: hover for taxa, click for details, double-click to add or edit calibrations in place
• Multi-window support — open multiple independent windows to work on different trees simultaneously (Ctrl+N)
• Convert calibrations to BEAST2 MRCAPrior XML
• Export modified trees back to MCMCTree Newick format

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Quick Start

Standalone Executable (no Python needed)

Download from Releases:

Platform	Download	Run
Linux	FossTree-linux.tar.gz	./FossTree
Windows	FossTree-windows.zip	FossTree.exe
macOS	FossTree-macos.tar.gz	FossTree.app

Install from Source

git clone https://github.com/piyumalanthony/FossTree.git
cd FossTree
pip install -e .
fosstree          # launch GUI

Requirements: Python 3.10+, PyQt5, matplotlib

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Usage

GUI

fosstree

1. Load a .tree / .nwk file (plain Newick or MCMCTree format)
2. Info tab shows taxa count, calibration table, tree stats
3. BEAST2 XML tab generates MRCAPrior XML blocks
4. Visualization tab renders the tree with interactive node editing

CLI

fosstree info my_tree.tree              # tree summary
fosstree convert my_tree.tree -o p.xml  # BEAST2 XML
fosstree view my_tree.tree              # render to PDF

Python API

from fosstree import NewickParser, BeastXMLGenerator, TreeVisualizer
from fosstree.utils import NewickWriter, parse_calibration
from fosstree.models import Calibration, LowerCalibration, GammaCalibration

# Parse
tree = NewickParser().parse_file("my_tree.tree")
print(tree.summary())

# Add calibrations (any MCMCTree type)
node = tree.calibrated_nodes[0]
node.calibration = Calibration(lower=5.0, upper=6.5)
# node.calibration = LowerCalibration(tL=0.06, p=0.1, c=1.0, pL=0.025)
# node.calibration = GammaCalibration(alpha=2, beta=5)

# Convert to BEAST2 XML
BeastXMLGenerator().write(tree, "priors.xml")

# Export back to MCMCTree Newick
NewickWriter().write_file(tree, "modified.tree")

# Visualize (cladogram or phylogram)
TreeVisualizer(show_branch_lengths=True).save(tree, "tree.pdf")

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Supported Calibration Types

Type	Format	Description
B	B(lower, upper[, pL, pU])	Lower & upper bounds
L	L(tL[, p, c, pL])	Lower (minimum) bound
U	U(tU[, pR])	Upper (maximum) bound
G	G(alpha, beta)	Gamma distribution
SN	SN(location, scale, shape)	Skew-normal
ST	ST(location, scale, shape, df)	Skew-t
S2N	S2N(p1, loc1, s1, sh1, loc2, s2, sh2)	Mixture of 2 skew-normals

Example tree:

((Human, Mouse)'B(0.616,1.646)', Chicken)'G(2,5)';

BEAST2 Mapping

MCMCTree	BEAST2 Distribution
B	Uniform
U	Uniform(0, tU)
G	Gamma
L	Exponential with offset (approximate)
SN, ST, S2N	Placeholder Uniform with warning comment

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Visualization Modes

• Cladogram (default) — all leaves aligned, topology only
• Phylogram (branch lengths checkbox) — branches scaled by length, dotted guide lines to aligned labels, tip distances shown on hover

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Dependencies

Package	Purpose
PyQt5	GUI
matplotlib	Visualization

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License

GNU General Public License v3.0

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Citation

FossTree: Fossil Calibration Annotation for Bayesian Molecular Dating
https://github.com/piyumalanthony/FossTree