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UShER Wiki
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Welcome to the manual for UShER package, that includes SARS-CoV-2 Phylogenetics tools UShER, matUtils, matOptimize, RIPPLES, strain_phylogenetics, and others. Please see the table of contents on the sidebar, or :doc:`click here <QuickStart>` for a quick tutorial on getting started.

.. toctree::
   :hidden:
   
   QuickStart.rst
   Installation.rst
   UShER.rst
   matUtils.rst
   matOptimize.rst
   ripples.rst
   bte.rst
   Strain_Phylogenetics
   tutorials
   presentations/presentations

.. _UShER:


UShER
=================

.. image:: usher_logo.png
    :width: 500px
    :align: center

UShER is a program for rapid, accurate placement of samples to existing phylogenies. Information on installation, usage, and features can be found :doc:`here <UShER>`. Our manuscript about UShER can be found `here <https://www.nature.com/articles/s41588-021-00862-7>`_.


.. _matUtils:


matUtils
============

matUtils is a toolkit for querying, interpreting and manipulating the mutation-annotated trees (MATs). Information on its usage can be found :doc:`here <matUtils>`.



matOptimize
============

matOptimize is a program to rapidly and effectively optimize a mutation-annotated tree (MAT) for parsimony using subtree pruning and regrafting (SPR) moves within a user-defined radius. Information on its usage can be found :doc:`here <matOptimize>`.


RIPPLES
============

RIPPLES is a program that uses a phylogenomic technique to rapidly and sensitively detect recombinant nodes and their ancestors in a mutation-annotated tree (MAT). Information on its usage can be found :doc:`here <ripples>`.


BTE
============

BTE is a separately packaged Cython API that wraps the highly optimized library underlying these other tools, exposing them for use in Python. Information about its usage can be found :doc:`here <bte>` and at its `repository <https://github.com/jmcbroome/BTE>`_.