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https://github.com/shuyib/phylogenetic-tree-study

Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7
https://github.com/shuyib/phylogenetic-tree-study

16s-rrna bokehplots hierarchical-clustering jupyter-notebook kenya machine-learning microorganism motif-analysis motif-discovery numpy-arrays pandas phylogenetics python scipy unsupervised-learning

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Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7

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# Phylogenetic-tree-study



Estimating Phylogenetic trees using 30 microorganisms (previously 6 organisms: review [data folder](https://github.com/Shuyib/Phylogenetic-tree-study/tree/master/data) and [notebook](https://github.com/Shuyib/Phylogenetic-tree-study/blob/master/Phylogenetic_trees_unsupervised_learning.ipynb). Looking at the 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7. Further we are looking at motifs and finding out what they do.



It is important to know these regions since they can potentially give use clues about the regions we can target for targeted DNA therapies.



# How to run in a virtual environment   

Make the virtual environment. When working in your own system   



```bash

python3 -m venv phylo-env   

```     

Activate the virtual environment.   



```bash

source phylo-env/bin/activate   

```   



Install packages. You need an email to be in your .bashrc file to run biopython.   



```bash

make install run_script

```   



In your terminal, in the directory where you cloned this repository. Run this command to run notebooks.   



```bash

jupyter notebook Phylogenetic_trees_unsupervised_learning.ipynb

```



Previously, we've not provided a codebook/data description file since one of the headings cover that in the notebook.

Otherwise, you can check out the [notebook](https://nbviewer.jupyter.org/github/Shuyib/Phylogenetic-tree-study/blob/master/Phylogenetic_trees_unsupervised_learning.ipynb) or the HTML file 

i've provided in the repository.    



# How to run project in Docker



Build DockerFile  

```bash

sudo docker build -t phylo-exp .

```   



Run the Docker image   

```bash

sudo docker run -it -p 8888:8888 --rm phylo-exp:latest

```  



# Add [data version control](https://dvc.org/doc/install)



Initialize dvc to the folder. To allow us to use dvc functionality to be used in the repo. NB. files will be created in the directory.    



```bash

dvc init

```  



Track changes to the different data files. The reason why we are doing this is because these files will change during the experiment especially if the investigator wants to try other experiments with more data.   



```bash

dvc add updated_data/data.md

dvc add updated_data/sequences.fasta

dvc add updated_data/sequence_metrics.csv

```  



Commit changes to save the changes that have occured in the repository.     



```bash

dvc commit

```