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🌲⚡ rapidtrees

Blazingly fast pairwise phylogenetic tree distance calculations — Robinson–Foulds, Weighted RF, and Kuhner–Felsenstein — powered by Rust

Crates.io PyPI CI Coverage License: MIT

Overview • Installing • Usage • Python API • Presence Matrix • Benchmarks


🗺️ Overview

rapidtrees computes pairwise tree distances from BEAST/NEXUS .trees files or plain multi-tree Newick files, and writes a labeled distance matrix. Three metrics are supported:

Metric Flag Output Description
Robinson–Foulds --metric rf integer Symmetric difference of bipartitions
Weighted RF --metric weighted float Branch-length-weighted bipartition difference
Kuhner–Felsenstein --metric kf float Euclidean distance on branch lengths

✨ Why rapidtrees?

  • 🦀 Rust core — splits as 128-bit fingerprints, compared as u32 IDs in a cache-friendly layout
  • 🔀 Parallel by default — powered by rayon, automatically scales across all cores
  • 🐍 Python bindings — drop into any Python/NumPy workflow via PyO3
  • 📦 No Rust toolchain required — pre-built wheels on PyPI for Linux, macOS, and Windows
  • 🗜️ Gzip output — stream directly to .tsv.gz without a separate compression step

🚀 Performance

Benchmarked on a ZIKA dataset (283 taxa · 4 000 trees · ~8 M comparisons) (non-gzipped output):

Metric Total time Throughput
Robinson-Foulds ~2.7 s ~3.0 M comparisons/sec
Weighted RF ~3.4 s ~2.3 M comparisons/sec
Kuhner-Felsenstein ~3.3 s ~2.3 M comparisons/sec

🔧 Installing

Pre-built wheels for Linux, macOS, and Windows. No Rust toolchain needed.

pip install rapidtrees

🦀 CLI (crates.io)

Install the standalone command-line binary. Requires the Rust toolchain.

cargo install rapidtrees

🎛️ Tuning the kernels

Every metric keeps a dense column only for splits held by a large enough share of the trees, and gives the rarer ones posting lists. The defaults were tuned on simulated posteriors. RAPIDTREES_RF_DENSE_SHARE (default 0.03) and RAPIDTREES_WEIGHTED_DENSE_SHARE (default 0.25) override them, for re-tuning on other data or hardware. They change the speed only, never a distance.

🛠️ From source

Prerequisites

  • Rust toolchain — for building the Rust core
  • pixi — for managing Python and R dependencies

Setup

git clone https://github.com/Joon-Klaps/rapidtrees.git
cd rapidtrees
# Set up environment — installs Python, R (with phangorn), and builds the package
pixi install

Development tasks

# Run Python API tests (includes R/phangorn cross-validation)
pixi run test-python

# Run Rust unit tests
pixi run test-rust

💻 Usage

rapidtrees \
  --input <path/to/file.trees> \
  --output <path/to/output.tsv[.gz]> \
  [--burnin-trees <N>] \
  [--burnin-states <STATE>] \
  [--use-real-taxa] \
  [--metric rf|weighted|kf] \
  [-q|--quiet]
Flag Description
-i, --input <INPUT> Path to a NEXUS .trees or plain Newick file (auto-detected)
-o, --output <OUTPUT> Output path. Use .gz suffix for gzip compression; - for stdout
-t, --burnin-trees <N> Drop the first N trees (default: 0)
-s, --burnin-states <STATE> Keep only trees with STATE > STATE (default: 0)
--use-real-taxa Map numeric taxon IDs via the TRANSLATE block
--metric <rf|weighted|kf> Distance metric (default: rf)
-q, --quiet Suppress progress messages (errors still go to stderr)

Input formats. --input takes either a NEXUS/BEAST trees file or a plain Newick file with one tree per line; the format is sniffed from the contents, not the extension. Newick files name nothing, carry no TRANSLATE block and no STATE_ labels, so their trees are named after the line they start on, and --burnin-states / --use-real-taxa have nothing to act on (--burnin-trees still works).

The output is a square TSV matrix where both the header row and first column contain tree names: <file_basename>_<tree_name> for NEXUS (e.g. hiv1_STATE_10000) and <file_basename>_line<n> for Newick (e.g. hiv1_line3). Use -o - to write to stdout for easy piping.

💡 Examples

Compute RF matrix → gzipped file
rapidtrees \
  -i tests/data/hiv1.trees \
  -o out/hiv1_rf.tsv.gz \
  --metric rf

# Reading in beast 0.003s
# Read in 162 taxons for 21 trees
# Creating tree bit snapshots 0.002s
# Determining distances using RF for 210 combinations
# Determining distances using RF 0.000s
# Writing to output 0.000s
Apply burn-in by tree count
rapidtrees \
  -i tests/data/hiv1.trees \
  -o out/hiv1_rf.tsv \
  -t 2

# Reading in beast 0.003s
# Read in 162 taxons for 19 trees
# Creating tree bit snapshots 0.001s
# Determining distances using RF for 171 combinations
# Determining distances using RF 0.000s
# Writing to output 0.000s

🐍 Python API

rapidtrees exposes four functions from its Rust core. All accept a Python iterator of newick strings, keeping memory constant regardless of tree count.

Function Returns
pairwise_rf_from_newick_iter (names, bytes) — RF matrix as flat uint32 bytes, row-major
pairwise_rf_with_snapshots_from_newick_iter (names, bytes, leaf_names, n_bip, bytes, bytes) — RF matrix + presence matrix + clade bitmasks
pairwise_wrf_from_newick_iter (names, list[float]) — Weighted RF, flat row-major
pairwise_wrf_with_snapshots_from_newick_iter (names, bytes, leaf_names, n_bip, bytes, bytes) — wRF matrix + branch-length matrix + clade bitmasks
pairwise_kf_from_newick_iter (names, list[float]) — Kuhner-Felsenstein, flat row-major
pairwise_kf_with_snapshots_from_newick_iter (names, bytes, leaf_names, n_bip, bytes, bytes) — KF matrix + branch-length matrix + clade bitmasks
import rapidtrees as rtd
import numpy as np

trees = [
    "(A:0.1,(B:0.1,C:0.1):0.1);",
    "(A:0.1,(C:0.1,B:0.1):0.1);",
    "((A:0.1,B:0.1):0.1,C:0.1);",
]
names = ["t1", "t2", "t3"]

tree_names, rf_bytes = rtd.pairwise_rf_from_newick_iter(
    names, iter(trees), [{}], [0, 0, 0]
)
rf = np.frombuffer(rf_bytes, dtype=np.uint32).reshape(len(tree_names), -1)

For BEAST .trees files, translate maps, the snapshot API, and multi-file usage see docs/python-api.md.


📦 Presence Matrix

Alongside a distance matrix, rapidtrees can hand back the presence matrix: which bipartition appears in which tree. That is everything the convergence diagnostics need (ESS, ASDSF, split frequencies), and it comes out of the same single parse as the distances.

Splits are identified by a 128-bit fingerprint, not by comparing leaf sets — that is what keeps building a tree linear in its taxon count rather than quadratic. Two distinct splits are merged if their fingerprints collide, with probability about e²/2¹²⁹ for e distinct splits in the run: 1.5 × 10⁻²³ at a hundred million splits, some nineteen orders of magnitude below the rate at which the machine's own RAM flips a bit unnoticed. Every run prints its own e and bound.

Bipartition column order is deterministic: columns are sorted in ascending Bitset order (lexicographic over u64 words, i.e. by leaf-index bit pattern), so the same tree set always produces the same column indices regardless of parse order.

What the presence matrix gives you

The presence matrix is sufficient for all major convergence diagnostics:

Diagnostic What you need
Pseudo ESS presence.mean(axis=0) per chain
ASDSF Per-chain split frequencies
Fréchet ESS RF distances via XOR of rows
WRF / KF distances Branch lengths — use pairwise_wrf_with_snapshots_from_newick_iter or pairwise_kf_with_snapshots_from_newick_iter

Note: sum(presence[i] XOR presence[j]) == RF(tree_i, tree_j) exactly.

Presence matrix from Python

Use pairwise_rf_with_snapshots_from_newick_iter to get the presence matrix alongside the RF distances, from one parse — see the Python API section above.

import rapidtrees as rtd
import numpy as np

import math

tree_names, rf_bytes, leaf_names, n_bip, pres_bytes, bip_clade_bytes = (
    rtd.pairwise_rf_with_snapshots_from_newick_iter(
        names, iter(newicks), translate_maps, map_indices
    )
)
n = len(tree_names)
presence = np.frombuffer(pres_bytes, dtype=np.uint8).reshape(n, n_bip).copy()

# Global split frequencies (for Pseudo ESS / ASDSF)
global_freq = presence.mean(axis=0)

# RF distance between any two trees — no recomputation needed
rf_01 = int((presence[0].astype(int) ^ presence[1].astype(int)).sum())

# Named presence matrix — decode clade bitmasks for column labels
bytes_per_bip = math.ceil(len(leaf_names) / 8)
bip_arr  = np.frombuffer(bip_clade_bytes, dtype=np.uint8).reshape(n_bip, bytes_per_bip)
bip_bool = np.unpackbits(bip_arr, axis=1, bitorder="little")[:, :len(leaf_names)]
col_labels = ["|".join(leaf_names[i] for i in np.where(bip_bool[j])[0]) for j in range(n_bip)]
import pandas as pd
df = pd.DataFrame(presence, index=tree_names, columns=col_labels)

⏱️ Benchmarks

Benchmarks were run on a MacBook Pro M1. Trees are parsed once and their interned split IDs are reused across all pairwise comparisons. Parallelism is provided by rayon — no manual thread management needed.

Show full benchmark table

Output of cargo bench --bench memory_time_benchmark

Taxa (N) Trees (T) Combinations Est. Memory Actual Memory Wall Time CPU Time
10 100 5.0K 13.96 KB 17.87 KB 172.29 µs 733.00 µs
10 1000 500.0K 139.65 KB 168.95 KB 5.94 ms 12.99 ms
10 10000 50.0M 1.36 MB 1.64 MB 717.43 ms 1.36 s
10 100000 5.0B 13.64 MB 16.40 MB 3.53 min 4.04 min
100 100 5.0K 133.59 KB 136.09 KB 244.42 µs 1.75 ms
100 1000 500.0K 1.30 MB 1.21 MB 17.49 ms 50.99 ms
100 10000 50.0M 13.05 MB 11.95 MB 1.08 s 4.81 s
100 100000 5.0B 130.46 MB 119.41 MB 4.29 min 9.86 min
500 100 5.0K 706.84 KB 713.93 KB 2.02 ms 3.08 ms
500 1000 500.0K 6.90 MB 5.89 MB 27.77 ms 216.87 ms
500 10000 50.0M 69.03 MB 57.84 MB 2.82 s 21.30 s
500 100000 5.0B 690.27 MB 577.28 MB 7.44 min 37.13 min
1000 100 5.0K 1.50 MB 1.51 MB 873.75 µs 5.63 ms
1000 1000 500.0K 15.03 MB 11.86 MB 51.22 ms 420.94 ms
1000 10000 50.0M 150.32 MB 115.30 MB 5.12 s 42.92 s
1000 100000 5.0B 1.47 GB 1.12 GB 11.26 min 74.74 min
2000 100 5.0K 3.50 MB 3.51 MB 1.14 ms 9.92 ms
2000 1000 500.0K 35.01 MB 24.15 MB 93.73 ms 838.01 ms
2000 10000 50.0M 350.06 MB 230.59 MB 9.42 s 1.38 min
2000 100000 5.0B 3.42 GB 2.24 GB 18.57 min 141.11 min
5000 100 5.0K 14.30 MB 12.43 MB 61.36 ms 83.85 ms
5000 1000 500.0K 143.02 MB 63.97 MB 224.40 ms 2.09 s
5000 10000 50.0M 1.40 GB 579.40 MB 22.45 s 3.44 min

Note: Weighted RF and KF produce floating-point matrices; RF produces integer matrices.


🔍 Troubleshooting

  • No trees parsed? Verify the input is a valid NEXUS .trees or Newick file and adjust --burnin-* settings.
  • Piping to other tools? Use -q to suppress timing messages on stdout.
  • Gzipped output not working? Ensure the output filename ends with .gz.

⚖️ License

rapidtrees is provided under the MIT License.

Release files for rapidtrees 0.10.0

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Source distribution (sdist)

Source distribution for rapidtrees 0.10.0
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File
rapidtrees-0.10.0-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ x86-64 Details
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rapidtrees-0.10.0-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
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rapidtrees-0.10.0-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
rapidtrees-0.10.0-cp313-cp313-macosx_10_12_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.12+ x86-64 Details
rapidtrees-0.10.0-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
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rapidtrees-0.10.0-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
rapidtrees-0.10.0-cp312-cp312-macosx_10_12_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.12+ x86-64 Details
rapidtrees-0.10.0-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
rapidtrees-0.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
rapidtrees-0.10.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details
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rapidtrees-0.10.0-cp311-cp311-macosx_10_12_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.12+ x86-64 Details
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rapidtrees-0.10.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARM64 Details

Total release size: 12.3 MB

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0.10.0 This release

30 release files

0.9.0

30 release files

0.8.0

28 release files

0.6.0

28 release files

0.5.1

28 release files

0.5.0

28 release files

0.2.3

30 release files

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