zenodoopen

Simulated pairs of nucleotide sequences for testing (alignment-free) genome distance estimate methods

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 d varying from 0.05 to 1.00 nucleotide substitutions per character (step = 0.05), the program <a href="http://abacus.gene.ucl.ac.uk/software/indelible/">INDELible</a> was used to simulate the evolution of 200 nucleotide sequence pairs with d substitution events per character under the models GTR and GTR+Γ. Each model was adjusted with three different equilibrium frequencies: <ul> <li>f1: equal frequencies, i.e. freq(A) = freq(C) = freq(G) = freq(T) = 0.25,</li> <li>f2: GC-rich, i.e. freq(A) = 0.1, freq(C) = 0.3, freq(G) = 0.4, freq(T) = 0.2,</li> <li>f3: AT-rich, i.e. freq(A) = freq(T) = 0.4, freq(C) = freq(G) = 0.1.</li> </ul> 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 <a href="https://zenodo.org/record/4034261/files/GTR.params.trees.tsv?download=1">GTR.params.trees.tsv</a> at <a href="https://zenodo.org/record/4034261">https://zenodo.org/record/4034261</a>). 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 INDELible <a href="http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml">manual</a>).   For each of the 20 evolutionary distances d = 0.05, 0.10, ..., 1.00, six XZ-compressed files containing 200 simulation data are available: <ul> <li><code>data-d-f1-nogam.tsv.xz</code>   data simulated under the model GTR with equilibrium frequencies f1</li> <li><code>data-d-f1-gamma.tsv.xz</code>   data simulated under the model GTR+Γ with equilibrium frequencies f1</li> <li><code>data-d-f2-nogam.tsv.xz</code>   data simulated under the model GTR with equilibrium frequencies f2</li> <li><code>data-d-f2-gamma.tsv.xz</code>   data simulated under the model GTR+Γ with equilibrium frequencies f2</li> <li><code>data-d-f3-nogam.tsv.xz</code>   data simulated under the model GTR with equilibrium frequencies f3</li> <li><code>data-d-f3-gamma.tsv.xz</code>   data simulated under the model GTR+Γ with equilibrium frequencies f3</li> </ul>   Each file is tab-delimited and contains the 18 following fields: <ul> <li><code>[1]   </code>   integer seed value specified to INDELible,</li> <li><code>[2-5] </code>   frequencies of T, C, A, G, respectively, specified to INDELible,</li> <li><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 INDELible,</li> <li><code>[11]   </code>   Γ shape parameter alpha (= 0 in the <code>nogam</code> files, i.e. GTR substitution model without Γ) specified to INDELible,</li> <li><code>[12]   </code>   length lgt1 of the first sequence seq1 (i.e. no. A, C, G, T in seq1),</li> <li><code>[13]   </code>   length lgt2 of the second sequence seq2 (i.e. no. A, C, G, T in seq2),</li> <li><code>[14]   </code>   no. sites in aligned sequences seq1 and seq2 (i.e. no. A, C, G, T and gap character states in seq1 or seq2),</li> <li><code>[15]   </code>   no. non-gapped sites (core sites) in aligned sequences seq1 and seq2,</li> <li><code>[16]   </code>   observed p-distance between aligned sequences seq1 and seq2 (i.e. no. nucleotide mismatches divided by no. core sites),</li> <li><code>[17]   </code>   aligned seq1 (containing indel gaps),</li> <li><code>[18]   </code>   aligned seq2 (containing indel gaps).</li> </ul> Of note, seq1 and seq2 (fields <code>[17-18]</code>) being aligned, these two entries are two strings with identical no. sites (field <code>[14]</code>). Gap character states (<code>-</code>) should be removed from seq1 and seq2 to obtain the unaligned sequences. _____ Criscuolo A (2020) On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Research, 9:1309. <a href="https://doi.org/10.12688/f1000research.26930.1">doi:10.12688/f1000research.26930.1</a>

ShareScore

28/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 16
Reuse readiness: 0
Engagement: 0

Topics

simulation genomes