This is a fork of the program Homo. Details about how to compile, install and use Homo Version 1.3 are available in the manual. Please direct errors, concerns and questions about the program to [email protected]

Several potential analyses were presented in the manual, which can be created for any dataset by directly using the output files from Homo.

1. Run Homo normally on a dataset, for instance, here using Dataset 16 from Whelan et al 2015.

2. Generate a PP plot using the R script pairwise_PPplot.R. The input is the summary.csv file from Homo and the output .pdf is automatically named as PP-plot.pdf.

   Rscript pairwise_PPplot.R whelan_d16_reorder_summary.csv

   The above command produces a PDF of the graph, named whelan_d16_reorder_summary_PP-plot.pdf.

3. Generate a heatmap of the p-values using the R script pvalue_heatmap.R. The input is the Pvalues.csv file and the output is automatically named as heatmap.pdf.

   Rscript pvalue_heatmap.R whelan_d16_reorder_Pvalues.csv