@hackage MutationOrder0.0.0.1

Most likely order of mutation events in RNA

  • Installation

  • Tested Compilers

  • Dependencies (27)

  • Dependents (0)

    • Package Flags

      debug
       (off by default)

      Enable bounds checking and various other debug operations at the cost of a significant performance penalty.

      debugoutput
       (off by default)

      Enable debug output, which spams the screen full of index information

Build Status

Determine the most likely order of mutations from one RNA sequence to another.

  1. Walter Costa, Maria Beatriz and Hoener zu Siederdissen, Christian and Tulpan, Dan and Stadler, Peter F. and Nowick, Katja
    Uncovering the Structural Evolution of the Human Accelerated Region 1
    2017, submitted
    preprint

Usage instructions

We assume that you have two Fasta files, from.fa and to.fa but they can be named however is convenient (say chimp.fa and human.fa). Each file has to contain exactly one sequence and both sequences have to be of the same length.

We then run

./MutationOrder --workdb from-to.json.gz --scoretype pairdistcen --onlypositive --outputprefix test

This will generate test.run, test-edge.eps, and test-meaorder.eps. The test.run file provides extensive output of the optimal path, the first-last probabilities, the edge probabilities, and the mea output. The two eps files give a graphical representation of the edge probabilities, for the meaorder in order of the path of maximum expected accuracy.

The --scoretype allows for mfe, centroid, pairdistcen, and pairdistmfe, which analyse possible evoluationary paths according to mfe energy, centroid energy, smallest base pair distances for each step in the centroid or mfe case.

Installation

Follow this link to the bottom of the page. Binaries are available for download and installation from sources via Haskell Stack are described.

Contact

Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/