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
|