.. phydms documentation master file, created by sphinx-quickstart on Tue Mar 31 11:35:01 2015. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Documentation for ``phydms`` ================================== `phydms`_ is a software package for **phy**\logenetic analyses using **d**\eep **m**\utational **s**\canning data to inform the substitution models. `phydms`_ can use :ref:`ExpCM` to describe the evolution of protein-coding genes for phylogenetic analyses and the detection of sites of biologically interesting selection. `phydms`_ is written in `Python`_ by `Bloom lab`_ (see the `full list of contributors`_). :ref:`installation` of `phydms`_ will install :ref:`phydms_prog`, which performs the phylogenetic analyses. It also installs :ref:`auxiliary_progs` that facilitate model comparisons and visualization of the results. All of these programs are installed as command-line executables. See :ref:`howtouse` for more details and a `tutorial `_ on how to use `phydms`_. The `phydms source code`_ is freely available under a `GPLv3`_ license. If you use `phydms`_, please cite the references in :ref:`acknowledgments`. Contents ------------ .. toctree:: :maxdepth: 1 installation howtouse phydms_prog auxiliary_progs ExpCM implementation phydmslib acknowledgments indices_and_tables .. include:: weblinks.txt