Profylo : benchmarking and application datas and scripts

This folder contains the experiment presented in the manuscript entitled "Profylo: a Python package for phylogenetic profile comparison and analysis" and published in the Journal of Molecular Evolution.Among other, it contains the phylogenetic profiles used in the analyses, the benchmarking results for the analyses and file describing the clusters of the the detailed use case, as well as some scripts needed to reproduce the results. The folder hierarchy is as follow:

Programming files- conda : Contains a file describing the set up of the conda environment use for the analysis- Notebooks : Contains the notebooks used for plotting the bencharmking results and to provide the analysis of the parsimony score.- scripts : Contains the python script that was used to obtain the benchmarking results from every distance matrix in this folder. The distance matricexs are located in distance_similarity_matrices and the benchmarking results in benchmark_results. Also contains the scripts used for KEGG module and pathway enrichment analysis.

Input files- datafiles : Contains external data file detailing KEGG pathways, GO terms for Human genes, paralogy relationship and any input files with information not containing in the profiles or the species tree. - profiles : Containe the phylogenetic files, as binary matrices, used in the paper on the three dataset described in the manuscript- trees : Contains the newick species tree used with the profiles in some of the analysis detailed in the paper

Output files- distance_similarity_matrices: Contains the files generated by using Profylo on the phylogenetic profiles in the profiles folder, with all methods available in profylo and for PCS and SVD, a variation of parameters.- benchmark_results : Contains the files generated by the script compute_kegg_precisons from the script folder, on the distance and similarity matrices from the folder distance_similarity_matrices. These results were used as benchmark for the different methods in Profylo.- application : Contains files corresponding to the human proteome case study (composition of clusters, enrichments, figures etc.).