Analysis archive for: No Evidence of an Embedded Message in Human Ultraconserved DNA

Complete analysis archive for the study “No Evidence of an Embedded Message in Human Ultraconserved DNA: A Bounded Computational Search with Stated Detection Limits” (Pappolla MA, submitted to Life, manuscript life-4649742). The archive contains the analysis code (Python with C inner loops), the input sequences (the 481 canonical ultraconserved elements of Bejerano et al. 2004 and their exonic labels; the pilot blocks derived from the Faircloth laboratory uce-probe-sets repository), the confirmatory analysis plan written before the canonical elements were scored, every random seed, the statistics of every shuffled comparison set (500 sets per data set, extended to 2000 for the canonical elements), all derived result files for the pilot and confirmatory stages and for the analyses added in peer review (overlap split, exon stratification with codon-phase-preserving and trinucleotide-permutation null models, implantation detection rates for text and mathematical signals), the independent verification record for all 24 statistics, the figures, and the sequence data sets and planted test sequences. README.txt gives the layout and the commands to reproduce every result; SEEDS.txt lists every random seed. Version 1.1 adds the trinucleotide-permutation null results for the non-exonic and the combined exonic-or-possibly-exonic strata (Table 6 of the manuscript).