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Reproducibility Information

This README describes how to reproduce the experiments related to PLA-complexity that are included in our biorxiv preprint. RefSeq_dataset.csv file contains the RefSeq IDs, Kingdom, alpha and beta values of Table 5. RefSeq_7Genomes.csv contains the RefSeq IDs of the genomes from Table 6. RefSeq_ID_List.txt contains the RefSeq IDs of the 549 genomes that were used for analyzing the pla-complexity.

Requirements

  • R (for finding the alpha and beta value (from pla-complexity) from segments vs eps curve fitting)

Fitting Segments

To find the fitted degree (alpha) and fitted constant (beta) values, fit_segments.R can be used. First, the epsilon values vs number of segments needs to be listed in a text file. (one such example is Gorilla.segments.txt). Then, list this file path and the genome length (each at a different line) in fit_segment_file.txt. (similar to fit_segment_file.txt). Then, running fit_segments.R will output the goodness of fits as well as the alpha and beta values.