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 Installation for additional details.

Dependencies

• python 2.7.x
• hyphy 2 <http://www.datam0nk3y.org/hyphy/>
• numpy 1.3.x
• scipy 0.9.0
• dendropy 3.9.0

Optional

One of the following is needed to produce graphical output. rpy2 provides richer graphics.

• rpy2 2.2.2
• matplotlib 1.0