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133 supplements.
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BIOINF 17-012: Expansion of Gene Clusters, Circular Orders, and the Shortest Hamiltonian Path Problem
Sonja J. Prohaska, Sarah J. Berkemer, Fabian Gärtner, Thomas Gatter, Nancy Retzlaff, The Students of the Graphs & Biological Networks Lab 2017, Christian Höner zu Siederdissen, Peter F. Stadler
Simulated Data
Name Description Link
simulation.py
All data are simulated and analyzed with this python script.
Download
Only duplications events; 1 percent mutation rate.
Name Description Link
sim.create
The overview of the simulation steps.
Download
sim.fa
The simulated sequences.
Download
sim.dis
The distance matrix that is used for Gene-CluEDO.
Download
sim.nex
The nexus file that is used for NeighborNet.
Download
Only unequal crossing over events; 1 percent mutation rate.
Name Description Link
sim.create
The overview of the simulation steps.
Download
sim.fa
The simulated sequences.
Download
sim.dis
The distance matrix that is used for Gene-CluEDO.
Download
sim.nex
The nexus file that is used for NeighborNet.
Download
Only unequal crossing over events; 5 percent mutation rate.
Name Description Link
sim.create
The overview of the simulation steps.
Download
sim.fa
The simulated sequences.
Download
sim.dis
The distance matrix that is used for Gene-CluEDO.
Download
sim.nex
The nexus file that is used for NeighborNet.
Download
Only unequal crossing over events; 10 percent mutation rate.
Name Description Link
sim.create
The overview of the simulation steps.
Download
sim.fa
The simulated sequences.
Download
sim.dis
The distance matrix that is used for Gene-CluEDO.
Download
sim.nex
The nexus file that is used for NeighborNet.
Download
Only unequal crossing over events; 15 percent mutation rate.
Name Description Link
sim.create
The overview of the simulation steps.
Download
sim.fa
The simulated sequences.
Download
sim.dis
The distance matrix that is used for Gene-CluEDO.
Download
sim.nex
The nexus file that is used for NeighborNet.
Download
Real Data
Hox gene cluster
Name Description Link
original.fa
The original file that contains the downloaded Sequences.
Download
tcoffee.aln
The alignment that is calculated with tcoffee.
Download
dialign.fa
The alignment that is left after the cleaning with Dialign.
Download
dialign.dis
The distance matrix that is used for Gene-CluEDO.
Download
dialign.nex
The nexus file that is used for NeighborNet.
Download
PSG gene cluster
Name Description Link
original.fa
The original file that contains the downloaded Sequences.
Download
tcoffee.aln
The alignment that is calculated with tcoffee.
Download
cycle.run
The cycle order that is calculated with Gene-CluEDO and used with noisy.
Download
noisy_idx.txt
The filter that noisy applied.
Download
noisy.fa
The alignment that is left after the cleaning with noisy.
Download
noisy.dis
The distance matrix that is used for Gene-CluEDO.
Download
noisy.nex
The nexus file that is used for NeighborNet.
Download
α-Rhox gene cluster
Name Description Link
original.fa
The original file that contains the downloaded Sequences.
Download
tcoffee.aln
The alignment that is calculated with tcoffee.
Download
cycle.run
The cycle order that is calculated with Gene-CluEDO and used with noisy.
Download
noisy_idx.txt
The filter that noisy applied.
Download
noisy.fa
The alignment that is left after the cleaning with noisy.
Download
noisy.dis
The distance matrix that is used for Gene-CluEDO.
Download
noisy.nex
The nexus file that is used for NeighborNet.
Download
ADH gene cluster
Name Description Link
original.fa
The original file that contains the downloaded Sequences.
Download
tcoffee.aln
The alignment that is calculated with tcoffee.
Download
cycle.run
The cycle order that is calculated with Gene-CluEDO and used with noisy.
Download
noisy_idx.txt
The filter that noisy applied.
Download
noisy.fa
The alignment that is left after the cleaning with noisy.
Download
noisy.dis
The distance matrix that is used for Gene-CluEDO.
Download
noisy.nex
The nexus file that is used for NeighborNet.
Download
