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TreeTime command line usage
===========================
TreeTime implements a command line interface (for details, see `Command-line API <commands.html>`_) that allow estimation of time scaled phylogenies, ancestral reconstruction, and analysis of temporal signal in alignments.
The command interface is organized as the main command performing time-tree estimation as
.. code:: bash
treetime --tree tree_file --aln alignment --dates dates.tsv
with other functionalities available as subcommands
.. code:: bash
treetime {ancestral, clock, homoplasy, mugration, arg, version}
TreeTime can use full alignments in `fasta` or `phylip` format or work of VCF files.
For each of the different subcommands, we prepared tutorials listed below.
These tutorials use example data provided in the github-repository
`github.com/neherlab/treetime_examples <https://github.com/neherlab/treetime_examples>`_.
.. toctree::
:maxdepth: 1
tutorials/timetree
tutorials/ancestral
tutorials/clock
tutorials/mugration
tutorials/homoplasy
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