In extracting the isochores from chromosome FASTA files, we used the following IsoFinder parameters:

  • Significance statistical level: 0.99 (p-value ≤ 0.01)
  • Significance method to compute p-values: p3 (parametric maximum value)
  • Coarse-graining level: 3000 bp


To extract the isochores from human chromosome 1, we used the following syntax on the command line:

isofinder chr1.fa 0.99 p3 3000 output_chr1.txt