Title : Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

Authors: Chris Papadopoulos, Isabelle Callebaut, Jean-Christophe Gelly, Isabelle Hatin, 
		Olivier Namy, Maxime Renard, Olivier Lespinet, Anne Lopes


Directory : Papadopoulos_Supplemental_Code1_Data

This directory contains all the homemade scripts and raw data that were used for this
analysis. The data are already organized into tables so that they can be easily read 
by R software. 

# --------------------------------- #
For the extraction of the non coding ORFs the tool ORFtrack was used with the default parameters.

For the calculation of the foldability,disorder and aggregation propensity of the sequences 
the tool ORFplot was used.

Both these tools are part of the package ORFmine that can be downloaded and installed easily 
from here : https://github.com/i2bc/ORFmine 
# --------------------------------- #


		Script_and_data_for_figures : 
			
			In this directory there are all the necessary data and script in order to repeat all the 
			analyses and generate all the figures of the results (and supplemental) presented 
			in the manuscript. All the data files can be found in the directory inputs. 
			All the figures are generated by the R script Papadopoulos_et_al_ANALYSIS.R and will be
			stored in the outputs directory. 
				
		De_novo_genes_ancestral_reconstruction :
		
			 In this directory there are all the necessary data and script in order to 
			 reproduce the ancestral reconstruction analysis of the 70 de novo genes. 
			 All the intermediate files generated by the analysis are given but following 
			 the pipeline proposed they can be regenerated.  
			 
		Random_sequences : 
		
			In this directory there are all the data of random sequences that were generated
			in order to test the neutrality of our results. The random sequences were 
			generated with homemade scripts. 





