Command-line versions


Unzip the files (Windows) or (Linux Debian) on a local directory, then obtaining the executable file 'isofinder'.



On a command-line window (DOS), change to the working directory containing the data and type:

<path> isofinder <DNA file> <Sig.Level> <Sig.Method> <Win.Size> <File out>

Linux Debian:

Open a terminal and type:

    <path> isofinder <DNA file> <Sig.Level> <Sig.Method> <Win.Size> <File out>


      • DNA File: File contaning the DNA sequence (EMBL,GenBank and FASTA formats are allowed)
      • Significance level: Statistical significance required to accept a new cut (e.g. 0.99 will accept less cuts than 0.95)
      • Window size for coarse graining: Window size to filter out short-scale heterogeneities
      • Method to compute the significance: Several methods to estimate the significance of a new cut (see: Oliver et al., Nucleic Acids Research 32, W287-W292, 2004 for details):
          • r Randomization (slow!)
          • p1 Parametric (t-student)
          • p2 Parametric (t-student) with different variances
          • p3 Parametric for maximum value
      • Output file: File to write the LHGR list in ASCII.

When the segmentation is finished the program generates the following files:

  1. iso_DNAfile.coo: List with LHGR's coordinates (ASCII)
  2. iso_DNAfile.html: List with LHGR's coordinates (HTML)