vappiah/create-phylogenetic-trees

Create Phylogenetic-trees

Description

This repository is a collection of scripts that can be used to generate phylogenetic trees.

Dependencies

Operating System

Linux, MacOS

Software

MUSCLE
PhyML
Python3.6+
    pip3
    virtualenv
    matplotlib
    biopython

Usage

download github repository

git clone https://github.com/vappiah/create-phylogenetic-trees

cd to the directory

cd create-phylogenetic-trees

add execution rights to the scripts

chmod +x *.{sh,py}

download and set up analysis environment

./download_tools.sh

test installation. You should have the version number and path to the followiing tools and libraries

muscle,phyml, python(matplotlib,biopython,pydot,networkx)

./test_tools.sh

its time to start analysis

confirm that you have your sequences

ls sequences

check how many sequences are there

ls sequences/*.fasta | wc -l

combine all the fasta files to a single file. a file called allseqs.fasta will be created and some the sequence in it will be displayed

./combine_fasta.sh sequences

Perform Multiple Sequence Alignment using MUSCLE

#This proceeds in two stages. Alignment and refining of alignment. Two files will be #generated the initial alignment file (allseqs.msa.fasa) and the refined (allseqs.refined.phylip).

./multiple_align.sh allseqs.fasta

Use PHYML to generate the phylogenetic-tree. Input file will be allseqs.refined.phylip.

#two files will be gerated. the maximlan likelihood tree(phyml_tree.txt) in newick format and model parameters (phyml_stats.txt)

./generate_phylo.sh allseqs.refined.phylip

Use python to draw the phylogenetic tree. Image will be saved in two formats (Phylo.jpg and Phylo.svg)

#activate the python environment

source phylo/bin/activate

#run the python script to generate phylo tree

python3 draw_phylo.py phyml_tree.txt

#you can view the phylogenetic tree. congratulations for performing a phylogenetic analysis. cheers!!!!!!!