https://github.com/thibaultlatrille/convergentdnds
https://github.com/thibaultlatrille/convergentdnds
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/thibaultlatrille/convergentdnds
- Owner: ThibaultLatrille
- Created: 2024-07-05T15:32:55.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-11-07T09:36:30.000Z (12 months ago)
- Last Synced: 2025-06-11T14:58:51.388Z (5 months ago)
- Language: Python
- Size: 859 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# **ConvergentdNdS**
The simulator [SimuEvol](https://github.com/ThibaultLatrille/SimuEvol) is required to generate the alignments.
## Installing *SimuEvol*
Install the compiling toolchains:
```
sudo apt install -qq -y make cmake clang
```
In the root folder of **ConvergentdNdS**, clone and compile the C++ code for *SimuEvol*
```
git clone https://github.com/ThibaultLatrille/SimuEvol && cd SimuEvol && make tiny && cd ..
```
## Replicate experiments
Running `snakemake` will generate the alignments for the experiment described `config/config.yaml`:
```
snakemake -j ${CPU} -k
```
To run the experiments for all the configurations in the `config` folder, you can use the following script:
```
CPU=8
for EXPERIMENT in config/Mammals*.yaml; do
cp -rf "${EXPERIMENT}" "config/config.yaml"
snakemake -j ${CPU} -k
done
```
Running the script `dataset.py` will create a folder `dataset` containing the alignments (in fasta format), the tree used to generate the simulations (`rootedtree.OrthoMam.nhx`), and a `dataset.csv` table which contains the relationships between the name of the fasta and the parameters that were used for the simulations.