.. _introduction:

************
Introduction
************

Purpose
=======

tapir_ is a "Phylogenetic Informativeness Calculator
for Marker Evaluation" - in short tapir_ does just what its acronym says -
calculates phylogenetic informativeness (PI) for a given set of phylogenetic
markers, using the formulas derived within [Townsend:2007]_.  tapir_ also
includes helper programs to plot the output of the program in several
different fashions using either R_ and ggplot2_ or matplotlib_.

Features
========

PhyDesign_ is the original implementation of Townsend's algorithms for
computing PI.  tapir_ is an alternative implementation, complementing
PhyDesign_ and differing in the folliowing ways:

- tapir_ selects the most appropriate finite-sites substitution model
  for input alignments, prior to inputting those rates and the base
  frequencies to the PI computation

- tapir_ is written to take advantage of optimized programming libraries
  and multicore architectures to return data from hundreds to thousands
  of loci very rapidly

- tapir_ enables rapid re-analysis of data from intermediate results
  stored in JSON_ format.  Meaning that once you've esimated the site
  rates for a given set of alignments, you do not need to re-analyze all
  of the input data to evaluate a new set of discrete times or time intervals

- tapir_ collects results across all loci in a SQL database, easing data
  summary and subsequeny analyses involving hundreds to thousands of loci

- tapir_ runs locally with reasonably minimal dependencies


Availability
============

We provide several methods of installing eddittag, see
:ref:`installation` for additional details.


Dependencies
============

- `python 2.7.x <http://www.python.org>`_
- `hyphy 2 <http://www.datam0nk3y.org/hyphy/>`
- `numpy 1.3.x <http://numpy.scipy.org>`_
- `scipy 0.9.0 <http://scipy.org>`_
- `dendropy 3.9.0 <http://packages.python.org/DendroPy/>`_

Optional
--------

One of the following is needed to produce graphical output.  rpy2_
provides richer graphics.

* `rpy2 2.2.2 <http://rpy.sourceforge.net/rpy2.html>`_
* `matplotlib 1.0 <http://matplotlib.sourceforge.net/>`_

.. _tapir: https://github.com/faircloth-lab/tapir
.. _rpy2: http://rpy.sourceforge.net/rpy2.html
.. _PhyDesign: http://phydesign.townsend.yale.edu/
.. _R: http://www.r-project.org/
.. _ggplot2: http://had.co.nz/ggplot2/
.. _matplotlib: http://matplotlib.sourceforge.net/
.. _JSON: http://www.json.org/