README.md

Phylo Flow

Description

This tool, developed within the scope of ASB.

Requirements

• at least one txt files with ascn number;
• Python & BioPython
• Mafft ;
• Modeltest-ng ;
• Raxml-ng ;
• Toytree ;
• Snakemake ;

txt file formart

#TxT formart
Sequence_name;ascn_number

#Example
Paramacrobiotus_gadabouti_sp._nov._MD50.1;OP394210

Installation

# Download the project
wget https://github.com/Rendrick27/PhyloFlow/archive/refs/heads/main.zip

# Unzip the folder
unzip main.zip

Then copy your .txt files into ascn folder.

Usage

# Navigate to the Snakemake directory
cd main.zip

Then, run the following command:

snakemake --use-conda all --cores 1

After that it will show a Tree.svg

Docker

Build it

docker build -t {image_name} .

docker run -it --name {container_name} {image_name} /bin/bash

Pull docker image

docker pull rendrick27/phylo_flow:latest

Settings

You may adjust settings in the Snakemake file, such as threads and bootstraps in params, but remember that using more threads may cause more issues.

Credits

Rendrick Carreira - 201901365

License

GPLv3