Publications - Supplemental material

Please find below supplemental material corresponding to publications of our group. Currently, we list 116 supplements. If you have problems accessing electronic information, please let us know:

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This supplement is also available at http://www.bioinf.uni-leipzig.de/publications/supplements/17-012
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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 Gartner, Thomas Gatter, Nancy Retzlaff, The Students of the Graphs and Biological Networks Lab 2017, Christian Honer zu Siederdissen, Peter F. Stadler

Simulated Data

NameDescriptionLink
simulation.py All data are simulated and analyzed with this python script. Download

Only duplications events; 1 percent mutation rate.

NameDescriptionLink
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.

NameDescriptionLink
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.

NameDescriptionLink
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.

NameDescriptionLink
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.

NameDescriptionLink
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

NameDescriptionLink
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

NameDescriptionLink
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

NameDescriptionLink
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

NameDescriptionLink
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