#Phasterate Paper Data Compilation

##Description This repo includes several scripts and all data: multiple sequence alignments, trees, along with conservation scores and p-values.

##Folders

Scripts/ This folder includes scripts to compute p-values from likelihood data and make volcano plots.

MakeGraph/ This folder includes the tex file to create graphs described above. Notice LaTex is required as well as the TexShade package: https://www.ctan.org/pkg/texshade?lang=en

Sample output and input data is included.

FittedData/ Data from the paper used to fit F84 and F84e models, as well as fitted models, computed likelihoods, and p-values.

InnerNodeData/ Data generated by running phyloP on several fake alignments to see what the probabilities at the inner nodes looked like.