scphylo-tools: a python toolkit for single-cell tumor phylogenetic analysis
scphylo-tools is a comprehensive Python toolkit designed for single-cell tumor phylogenetic analysis. It integrates efficient implementations of state-of-the-art methods to infer evolutionary trees from single-cell genotype data.
Features
Phylogenetic Inference: Wrappers and implementations for state-of-the-art inference methods.
API & CLI: Provides a Python API as well as command-line tools.
Visualization: Built-in visualization tools.
Datasets: Access to available datasets.
Ease of Use: A unified Python interface for complex phylogenetic workflows.
Installation
Install the Python package from PyPI:
pip install scphylo-toolsFor development and the complete native stack, use Pixi. Pixi installs Python together with Graphviz, R, rpy2, ggtree, ggtreeExtra, graph-tool, and MPI from the lockfile:
git clone https://github.com/faridrashidi/scphylo-tools
cd scphylo-tools
pixi install --locked
pixi run testThe locked Pixi environments support Linux and macOS. On Windows, use WSL for the complete native and R plotting stack.
The regular PyPI wheel and source distribution remain available for users who only need the Python package. See the installation guide for the complete development environment and plotting details.
Documentation
Detailed documentation and tutorials are available at Read the Docs.
1 maintainer
Release files for scphylo-tools 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scphylo_tools-0.1.1.tar.gz | 24.3 MB | Details |
Built distributions (wheels)
Total release size: 383.3 MB
Release files / scphylo_tools-0.1.1.tar.gz
| Download URL | scphylo_tools-0.1.1.tar.gz |
|---|---|
| Size | 24.3 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
471c00e7df9eb71741a6521e261d76a91fd0c943dc52eff5bfc9f2a9330db058
|
|
BLAKE2b-256 checksum How to use checksums |
9822cfe53abca8ccaa85aac185ebcbc47fd6f2cbed8238c884084790b0cde767
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp313-cp313-musllinux_1_2_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp313-cp313-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 35.2 MB |
| Tags | CPython 3.13 Linux musl 1.2+ x86-64 |
|
SHA-256 checksum How to use checksums |
f3a16ff6d41ace73cc7a4173aaa3f757715405e21fe137485adfe52a272eb311
|
|
BLAKE2b-256 checksum How to use checksums |
20a06cdae6d29b06a121230ddde0d3765b5bc6f972a10791dca8a45e4e293991
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 34.3 MB |
| Tags | CPython 3.13 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
ece520c0760f7e98ec8730c1003a79b7f640308efa8b48977c8c672c91f66e1c
|
|
BLAKE2b-256 checksum How to use checksums |
7063694c720b2fce322bf60a8180d847cecbcbdf751ad3d0e2ad2c4b4b621a5a
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp313-cp313-macosx_11_0_arm64.whl
| Download URL | scphylo_tools-0.1.1-cp313-cp313-macosx_11_0_arm64.whl |
|---|---|
| Size | 25.1 MB |
| Tags | CPython 3.13 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
5938648e98bcc5e5098b5da1430e730404eecc2d378ff8b9ff3367582f9c4972
|
|
BLAKE2b-256 checksum How to use checksums |
34c3d685b0bd9b999b2db53ac253d4d1be6a189e998a34a7a235b87939fc235e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp313-cp313-macosx_10_13_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp313-cp313-macosx_10_13_x86_64.whl |
|---|---|
| Size | 25.1 MB |
| Tags | CPython 3.13 macOS 10.13+ x86-64 |
|
SHA-256 checksum How to use checksums |
4380f7869fe9a434998d64cbb95820ea0fe2db333ac4e20e6cb042695ca449ab
|
|
BLAKE2b-256 checksum How to use checksums |
ea5a898d606f94c6749a854652f584dd8609666a4ae614eb428fea4862631335
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp312-cp312-musllinux_1_2_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp312-cp312-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 35.2 MB |
| Tags | CPython 3.12 Linux musl 1.2+ x86-64 |
|
SHA-256 checksum How to use checksums |
1b8fae9261a47261a1115b6b7cda21d645dee8695774f478399e3f2a507ec9a3
|
|
BLAKE2b-256 checksum How to use checksums |
7f6b759812b700ff445faaf7be1464a0ab15525801b55544510565b46bb82b8a
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 34.3 MB |
| Tags | CPython 3.12 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
c164e3508043c3c49e310558a6e36428d31f1b2490b2daa1b8a342ed008f73f8
|
|
BLAKE2b-256 checksum How to use checksums |
1ea12eab7946499767bc53feaccbf5f26d753db65b530a43799b1260782193c5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | scphylo_tools-0.1.1-cp312-cp312-macosx_11_0_arm64.whl |
|---|---|
| Size | 25.1 MB |
| Tags | CPython 3.12 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
9b6cc10a6236160a10771a2bb8ff5dcc4dfe2f5a260f2791ac052b6135d37bda
|
|
BLAKE2b-256 checksum How to use checksums |
be76480f286e28caff47f2a4cd7ccd8eb96b718ddc6ad86fe052393f724694f9
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp312-cp312-macosx_10_13_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp312-cp312-macosx_10_13_x86_64.whl |
|---|---|
| Size | 25.1 MB |
| Tags | CPython 3.12 macOS 10.13+ x86-64 |
|
SHA-256 checksum How to use checksums |
88ca6e40be4c8cdc054963414efb7f6f23405db14322558d22c14c67a28cdd08
|
|
BLAKE2b-256 checksum How to use checksums |
2ec412950802c8f6ef3bb9f268a3aaacd74ae0b3e8a2030a43305fc5584e3a69
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp311-cp311-musllinux_1_2_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp311-cp311-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 35.1 MB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-64 |
|
SHA-256 checksum How to use checksums |
91acaa3d185a0f40864af68d27d83f4178564340aa6ab0ad4290af4481423177
|
|
BLAKE2b-256 checksum How to use checksums |
6d5b2720c393e53f5e3249bc8ceb3fd3159827513270d5b40ffab204b3b50fce
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 34.3 MB |
| Tags | CPython 3.11 Linux glibc 2.27+ x86-64 Linux glibc 2.28+ x86-64 |
|
SHA-256 checksum How to use checksums |
3d249d1ca920dc036c9b665d4b291c8390404135e19848ca4037d3dbd50c7284
|
|
BLAKE2b-256 checksum How to use checksums |
0ce9f05590fd304918e848b43d9435e215599d1d348dd3e31276c6e349cfe32e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | scphylo_tools-0.1.1-cp311-cp311-macosx_11_0_arm64.whl |
|---|---|
| Size | 25.1 MB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
3a3f4b6f9e77a6b1347e7982f4fcde6ebd23e84e756b2d9f5a3cd2cacd830c47
|
|
BLAKE2b-256 checksum How to use checksums |
e782087c524a0a53706c71a757913218c724cd131afc87540480fbe1a2c8e000
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / scphylo_tools-0.1.1-cp311-cp311-macosx_10_9_x86_64.whl
| Download URL | scphylo_tools-0.1.1-cp311-cp311-macosx_10_9_x86_64.whl |
|---|---|
| Size | 25.1 MB |
| Tags | CPython 3.11 macOS 10.9+ x86-64 |
|
SHA-256 checksum How to use checksums |
34480f65a5432b9681237a3f85049002d8009e29eb3c414d471ba910a388cdf2
|
|
BLAKE2b-256 checksum How to use checksums |
a5490ae25db2ce4907b97a06fc8ffd000058c09f028b0f80e4ab5bb9b8fcf3b8
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
