EqualTDRL

EqualTDRL Overview

EqualTDRL is a tool for illustrating all equivalent parsimonious tandem duplication random loss (TDRL) rearrangement scenarios between two given mitochondrial gene orders where at least one of the gene orders can be rearranged into the other one by one TDRL rearrangement.

EqualTDRL relies on the ggplot2 package of the open source programming language R.

Downloads

Download here

Installation:

  1. Install R (e.g., see https://www.r-project.org/)
  2. Install ggplot2 (e.g., see https://www.r-bloggers.com/installing-r-packages/)
  3. Download EqualTDRL
  4. Extract EqualTDRL.tar.gz (tar -zxvf equaltdrl.tar.gz)

EqualTDRL is executed from the command line using:

./equaltdrl.sh -f input_filename [-g restriction_filename -d]

Use equaltdrl.sh -h for more information.

Test:

For testing whether or not EqualTDRL is installed correctly, enter ./equaltdrl.sh -f example.fas. The outcome should be stored in NC_003057_NC_003343.pdf.

Feel free to send bug reports or any other kind of impressions or suggestions on EqualTDRL to

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Publication:

Tom Hartmann, Martin Middendorf, Matthias Bernt
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
BMC Bioinformatics 19, 192 (2018).