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 d varying from 0.05 to 1.00 nucleotide substitutions per character (step = 0.05), the program INDELible 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:
- f1: equal frequencies, i.e. freq(A) = freq(C) = freq(G) = freq(T) = 0.25,
- f2: GC-rich, i.e. freq(A) = 0.1, freq(C) = 0.3, freq(G) = 0.4, freq(T) = 0.2,
- f3: 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 INDELible manual).
For each of the 20 evolutionary distances d = 0.05, 0.10, ..., 1.00, six XZ-compressed files containing 200 simulation data are available:
data-d-f1-nogam.tsv.xz
data simulated under the model GTR with equilibrium frequencies f1data-d-f1-gamma.tsv.xz
data simulated under the model GTR+Γ with equilibrium frequencies f1data-d-f2-nogam.tsv.xz
data simulated under the model GTR with equilibrium frequencies f2data-d-f2-gamma.tsv.xz
data simulated under the model GTR+Γ with equilibrium frequencies f2data-d-f3-nogam.tsv.xz
data simulated under the model GTR with equilibrium frequencies f3data-d-f3-gamma.tsv.xz
data simulated under the model GTR+Γ with equilibrium frequencies f3
Each file is tab-delimited and contains the 18 following fields:
[1]
integer seed value specified to INDELible,[2-5]
frequencies of T, C, A, G, respectively, specified to INDELible,[6-10]
C-T, A-T, G-T, A-C, C-G rate parameters, respectivly (normalized such that A-G rate = 1), specified to INDELible,[11]
Γ shape parameter alpha (= 0 in thenogam
files, i.e. GTR substitution model without Γ) specified to INDELible,[12]
length lgt1 of the first sequence seq1 (i.e. no. A, C, G, T in seq1),[13]
length lgt2 of the second sequence seq2 (i.e. no. A, C, G, T in seq2),[14]
no. sites in aligned sequences seq1 and seq2 (i.e. no. A, C, G, T and gap character states in seq1 or seq2),[15]
no. non-gapped sites (core sites) in aligned sequences seq1 and seq2,[16]
observed p-distance between aligned sequences seq1 and seq2 (i.e. no. nucleotide mismatches divided by no. core sites),[17]
aligned seq1 (containing indel gaps),[18]
aligned seq2 (containing indel gaps).
Of note, seq1 and seq2 (fields [17-18]
) being aligned, these two entries are two strings with identical no. sites (field [14]
). Gap character states (-
) 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. doi:10.12688/f1000research.26930.1
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