Simulated nucleotide sequences for testing alignment-free genome distance estimates

This repository contains (12×500=)6,000 pairs of nucleotide sequences that have been simulated for testing alignment-free genome distance estimates, as described in Criscuolo (2019). Given an evolutionary distance d varying from 0.05 to 0.60 (step = 0.05), the program SeqGen was used to simulate the evolution of 500 nucleotide sequence pairs with d substitution events per character (GTR+Γ evolutionary model).

For each of the 12 evolutionary distances d = 0.05, 0.10, ..., 0.60, an XZ-compressed file containing 500 lines is available. Each line contains 18 fields separated by blank spaces:
  [1]     seed value used during simulation,
  [2]     true evolutionary distance d between the two simulated sequences,
  [3]     total number of simulated characters,
  [4]     number of non-indel characters with nucleotide mismatch,
  [5]     number of non-indel characters,
  [6-9]   A, C, G, T frequencies used during simulation,
  [10-15]   GTR parameters used during simulation,
  [16]     Γ distribution parameter used during simulation,
  [17-18]   two simulated sequences with indel events as gaps.

Of note, each pair of aligned sequences without gaps can be regenerated using SeqGen v1.3.4 with parameters from fields [1,3,6-16] and the following two-leaf model tree:

(t1:d,t2:0.000);

where d is given in field [2].

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Criscuolo A (2019) A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. Research Ideas and Outcomes, 5:e36178. doi:10.3897/rio.5.e36178