https://github.com/bebatut/evolution_genome_structure
https://github.com/bebatut/evolution_genome_structure
Last synced: 12 months ago
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- Host: GitHub
- URL: https://github.com/bebatut/evolution_genome_structure
- Owner: bebatut
- Created: 2019-12-19T16:16:07.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-05-27T08:37:37.000Z (about 6 years ago)
- Last Synced: 2025-02-08T04:18:27.476Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 3.48 MB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Test of different hypotheses for reductive genome evolution
===========================================================
**Input question**: What can cause a reductive genome evolution based on the hypotheses found in literature?
**Methodology**: In silico evolution experiments with [aevol (v6)](https://gitlab.inria.fr/aevol/aevol/-/tree/aevol_6) following the methodology explained in [Batut et al, 2015](https://link.springer.com/article/10.1186/1471-2105-14-S15-S11)
- Creation of wild-type populations (10 seeds?)
- Test of the different hypotheses (called scenarios)
- Change of 1 parameter on the WT populations
- Evolution with the new parameter
- Comparison of genome structure with the WT
# Simulations
## Required resources
-
## Requirements
- [conda](https://conda.io/miniconda.html)
- Dependencies for aevol: build tools (make, etc), compression library (zlib), Bo ost library, X libraries
For Ubuntu (on a new VM)
- Run dedicated script
```
$ bash src/prepare_ubuntu.sh
```
- Log out
- Create the conda environment:
```
$ conda env create -f environment.yml
```
## Run WT and scenarios
- Prepare aevol
```
$ bash src/prepare_aevol.sh
```
- Prepare and launch a WT
```
$ source activate aevol_scenario
$ python \
src/launch_simulation.py \
--simu wt \
--seed <0...9>
```
- Prepare and launch a scenario
```
$ (source activate aevol_scenario)
$ python \
src/launch_simulation.py \
--simu \
--seed <0...9>
```
Possible scenarios:
Scenario | Type of scenario | Shortcut for script
--- | --- | ---
Increase of the population size | Muller's ratchet | `pop+`
Reduction of population size | Muller's ratchet | `pop-`
Increase of selection pressure | Muller's ratchet | `sel+`
Reduction of population pressure | Muller's ratchet | `sel-`
Stop of the transfer | Muller's ratchet | `transfer-`
Increase of local mutation rates | Increase of mutation rates | `mut+`
Decrease of local mutation rates | Increase of mutation rates | `mut-`
Increase of rearrangement rates | Increase of mutation rates | `rear+`
Decrease of rearrangement rates | Increase of mutation rates | `rear-`
Stabilisation of the environment | Environmental changes | `stab-env`
Change of the environmental target | Environmental changes | `change-env`
Neutralization of one part of the environmental target | Environmental changes | `neut-env`
Removal of one part of the environmental target | Environmental changes | `env-`
# Analyses of the scenarios
- Launch Jupyter notebooks
```
$ (source activate aevol_scenarios)
$ jupyter notebook
```
- Open [http://localhost:8888](http://localhost:8888)