.. _contents:

#######################################
Scripts: Context Dependent Substitution
#######################################

This document is a companion to a manuscript contrasting the properties of two independent-tuple context dependent substitution model forms. The two model forms differ in their weighting of the instantaneous rate matrix, employing either nucleotide frequencies or tuple frequencies and are referred to as the NF and TF forms respectively.

The purpose of this document is to provide a more readable form of the key scripts used in this study with some additional commentary. An archive of the actual scripts and data generated/used in the study is also included as a companion directory. Running the analysis scripts requires installation of the modified version of PyCogent (distributed as Additional data file 1) and its dependencies. Running the visualisation and summary scripts requires matplotlib_ (version 0.98 or greater).

Data used in the study, both simulated and real sequence alignments, and the raw Python scripts are available on request from the `corresponding author`_.

The order of content listing matches the order of dicussion in the main manuscript.

.. _matplotlib: http://matplotlib.sourceforge.net
.. _`corresponding author`: Gavin.Huttley@anu.edu.au

.. TODO Tarball both the html dir and the actual mercurial repo into a single directory for inclusion as "Additional data file 2"

**Contents:**

.. toctree::
   :maxdepth: 2
   
   tf_affected_by_composition
   filter_masked_align
   fit_dinuc_gtr
   fit_dinuc_individ

##################
Indices and tables
##################

* :ref:`search`