.. Copyright (C) 2020  Momoko Hayamizu <hayamizu@ism.ac.jp>
..
.. This program is free software: you can redistribute it and/or modify
.. it under the terms of the GNU Lesser General Public License as
.. published by the Free Software Foundation, either version 3 of the
.. License, or (at your option) any later version.
..
.. This program is distributed in the hope that it will be useful,
.. but WITHOUT ANY WARRANTY; without even the implied warranty of
.. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
.. GNU General Public License for more details.
..
.. You should have received a copy of the GNU Lesser General Public
.. License along with this program.  If not, see
.. <http://www.gnu.org/licenses/>.

Treefit for Python - The first software for quantitative trajectory inference
=============================================================================

This is an implementation of `Treefit
<https://hayamizu-lab.github.io/treefit/>`_ in Python.

**Treefit** is a novel data analysis toolkit that helps you perform
two types of analysis: 1) checking the goodness-of-fit of tree models
to your single-cell gene expression data; and 2) deciding which tree
best fits your data.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   install
   getting_started
   api
   release_notes