/Tt_MA_supplement

Exploratory analysis of Tetrahymena MA experiment

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DOI

#Supplimentary file for our Tetrahymena mutation rate paper

This repo holds an Ipython Notebook containing an exploratory analysis into an unsual pattern affecting two lines of an MA experiment described in a forthcoming paper.

To limit the size of this repository, the T. thermophila reference genome, which is required to compile this notebook, is not included. It can be fetched from ciliate.org via

wget http://www.ciliate.org/system/downloads/T_thermophila_June2014_assembly.fasta -O data/tt-ref.fasta

The notebook can then be opened and edited via a web-browser by running ipython notebook

Alternatively, if make is installed on your system you can fetch the reference genome and compile the notebook into a PDF by typing make.