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Single-Cell Analysis, comparing pseudotime trajectories with tree alignment

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PyPI version Documentation Status DOI


Alignment of single-cell trajectory trees

Last updated: 2022-12-16

We present CAPITAL, a computational method for comparing pseudotime trajectories with tree alignment whereby trajectories including branches can be automatically compared.


  • CAPITAL (ver. 1.0.14) in Python


  • Python>=3.8 (Miniconda is recommended)
  • anndata>=0.7.4
  • graphtools
  • graphviz
  • h5py>=2.10
  • leidenalg
  • magic-impute
  • matplotlib==3.5.2
  • networkx<=2.8.3
  • pandas>=0.21
  • pydot
  • scanpy==1.9.1
  • scikit-learn
  • scipy>=1.4
  • scprep
  • tslearn

Install on Linux, Windows (WSL) and macOS

Create a new environment for CAPITAL (recommended):

conda create -n capital python=3.9 graphviz

Next, activate the environment and pull CAPITAL from PyPI:

conda activate capital
pip install capital


Read the documentation. CAPITAL uses a single-cell analysis toolkit Scanpy in its implementation so that one can also use Scanpy's useful functions including preprocessing, plotting and datasets in the CAPITAL environment.

Code Ocean

We also provide a Code Ocean compute capsule to reproduce our results.


Reiichi Sugihara, Yuki Kato, Tomoya Mori and Yukio Kawahara, Alignment of single-cell trajectory trees with CAPITAL, Nature Communications, vol. 13, 5972, 2022. [Link]

If you have any questions, please contact Yuki Kato. Graduate School of Medicine, Osaka University, Japan.

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