DOI: 10.5281/zenodo.4034462
title: Simulated pairs of nucleotide sequences for testing (alignment-free) genome distance estimate methods

description: This repository contains 24,000 pairs of nucleotide sequences (and associated parameters) that have been simulated for testing alignment-free genome distance estimates. Given an evolutionary distance <em>d</em> varying from 0.05 to 1.00 nucleotide substitutions per character (step = 0.05), the program <em>INDELible</em> was used to simulate the evolution of 200 nucleotide sequence pairs with <em>d</em> substitution events per character under the models GTR and GTR+Γ. Each model was adjusted with three different equilibrium frequencies: <em>f</em><sub>1</sub>: equal frequencies, i.e. freq(A) = freq(C) = freq(G) = freq(T) = 0.25, <em>f</em><sub>2</sub>: GC-rich, i.e. freq(A) = 0.1, freq(C) = 0.3, freq(G) = 0.4, freq(T) = 0.2, <em>f</em><sub>3</sub>: AT-rich, i.e. freq(A) = freq(T) = 0.4, freq(C) = freq(G) = 0.1. For each simulated sequence pair, model parameters (i.e. GTR: six relative rates of nucleotide substitution; GTR+Γ: six rates and one Γ shape parameter) were randomly drawn from 142 sets of parameters derived from real-case data (see file GTR.params.trees.tsv at https://zenodo.org/record/4034261). Initial sequence length was 5 Mbs, and an indel rate of 0.01 was set with indel length drawn from [1, 50000] according to a Zipf distribution with parameter 1.5 (see <em>INDELible</em> manual). For each of the 20 evolutionary distances <em>d</em> = 0.05, 0.10, ..., 1.00, six XZ-compressed files containing 200 simulation data are available: <code>data-d-f1-nogam.tsv.xz</code> data simulated under the model GTR with equilibrium frequencies <em>f</em><sub>1</sub> <code>data-d-f1-gamma.tsv.xz</code> data simulated under the model GTR+Γ with equilibrium frequencies <em>f</em><sub>1</sub> <code>data-d-f2-nogam.tsv.xz</code> data simulated under the model GTR with equilibrium frequencies <em>f</em><sub>2</sub> <code>data-d-f2-gamma.tsv.xz</code> data simulated under the model GTR+Γ with equilibrium frequencies <em>f</em><sub>2</sub> <code>data-d-f3-nogam.tsv.xz</code> data simulated under the model GTR with equilibrium frequencies <em>f</em><sub>3</sub> <code>data-d-f3-gamma.tsv.xz</code> data simulated under the model GTR+Γ with equilibrium frequencies <em>f</em><sub>3</sub> Each file is tab-delimited and contains the 18 following fields: <code>[1] </code> integer <em>seed</em> value specified to <em>INDELible</em>, <code>[2-5] </code> frequencies of T, C, A, G, respectively, specified to <em>INDELible</em>, <code>[6-10] </code> C-T, A-T, G-T, A-C, C-G rate parameters, respectivly (normalized such that A-G rate = 1), specified to <em>INDELible</em>, <code>[11] </code> Γ shape parameter <em>alpha</em> (= 0 in the <code>nogam</code> files, i.e. GTR substitution model without Γ) specified to <em>INDELible</em>, <code>[12] </code> length <em>lgt1</em> of the first sequence <em>seq1</em> (i.e. no. A, C, G, T in <em>seq1</em>), <code>[13] </code> length <em>lgt2</em> of the second sequence <em>seq2</em> (i.e. no. A, C, G, T in <em>seq2</em>), <code>[14] </code> no. <em>sites</em> in aligned sequences <em>seq1</em> and <em>seq2</em> (i.e. no. A, C, G, T and gap character states in <em>seq1</em> or <em>seq2</em>), <code>[15] </code> no. non-gapped sites (<em>core</em> sites) in aligned sequences <em>seq1</em> and <em>seq2</em>, <code>[16] </code> observed <em>p-distance</em> between aligned sequences <em>seq1</em> and <em>seq2</em> (i.e. no. nucleotide mismatches divided by no. <em>core</em> sites), <code>[17] </code> aligned <em>seq1</em> (containing indel gaps), <code>[18] </code> aligned <em>seq2</em> (containing indel gaps). Of note, <em>seq1</em> and <em>seq2</em> (fields <code>[17-18]</code>) being aligned, these two entries are two strings with identical no. <em>sites</em> (field <code>[14]</code>). Gap character states (<code>-</code>) should be removed from <em>seq1</em> and <em>seq2</em> to obtain the unaligned sequences. _____ Criscuolo A (2020) <em>On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference</em>. F1000Research, 9:1309. doi:10.12688/f1000research.26930.1