NAME - Sorts output files from by different criteria

SYNOPSIS [options] key [file]


-r, --reverse

Sort in reverse order.


Do not preserve the locus grouping but simply sort the windows.

-v, --version

Prints version information and exits.

-h, --help

Prints a short help message and exits.


Prints a detailed manual page and exits.

DESCRIPTION reads tab-delimited data files as generated by The files are sorted according to a key which is given at the command line as a mandatory argument. See below for a list of possible keys. By default ``better" hits are listed first (e.g. lower z-score or higher P). This can be changed by using the --reverse option. By default, the grouping in loci is preserved during sorting. For example if you sort by z-score, you get first the locus first whicht contains the window with the lowest z-score. If you simply want all windows sorted without considering the grouping use the --no-loci option.


  1. windowID

    Consecutive numbered ID for each window. BUG: currently window10 comes before window9 because it is sorted alphabetically.

  2. locusID

    The locus which this window belongs to. BUG: currently locus10 comes before locus9 because it is sorted alphabetically.

  3. seqID

    Identifier of the sequence (e.g. human.chr1 or contig42)

  4. start

    Start position of the reference sequence in the window

  5. end

    End position of the reference sequence in the window

  6. strand

    Indicates if the reference seqeunce is from the positive or negative strand

  7. N

    Number of sequences in the alignment

  8. columns

    Number of columns in the alignment

  9. identity

    Mean pairwise identity of the alignment

  10. meanMFE

    Mean minimum free energy of the single sequences as calculated by the RNAfold algorithm

  11. consensusMFE

    ``Consensus MFE" for the alignment as calculated by RNAalifold algorithm

  12. energyTerm

    Contribution to the consensus MFE which comes from the energy part of the RNAalifold algorithm

  13. covarianceTerm

    Contribution to the consensus MFE which comes from the covariance part of the RNAalifold algorithm

  14. combPerPair

    Number of different base combinations per predicted pair in the consensus seconary structure

  15. z

    Mean z-score of the sequences in the alignment

  16. SCI

    Structure conservation index for the alignment

  17. decValue

    Support vector machine decision value

  18. P

    RNA class probability as calculated by the SVM


 # combPerPair results.dat

Sort by ``combinations per pair" value, i.e. gives you the hits with the most compensatory mutations.


Stefan Washietl <>