https://github.com/thibaultlatrille/convergentdnds

https://github.com/thibaultlatrille/convergentdnds

Last synced: 1 day ago
JSON representation

• Host: GitHub
• URL: https://github.com/thibaultlatrille/convergentdnds
• Owner: ThibaultLatrille
• Created: 2024-07-05T15:32:55.000Z (3 months ago)
• Default Branch: main
• Last Pushed: 2024-07-08T19:35:02.000Z (3 months ago)
• Last Synced: 2024-07-10T00:40:49.127Z (3 months ago)
• Language: Python
• Size: 125 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

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 release && 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