DNA Sequence Analysis: Phylogenetic Trees of TP53 and EPM2A

Phylogenetic analysis of two human genes, TP53 and EPM2A. For each gene, homologous sequences were collected, aligned, and used to build a phylogenetic tree.

Repository contents

File	Description
EPM2A.fasta	Reference sequence for EPM2A
epm2a_homologs.fasta	Homologous sequences collected for EPM2A
epm2a_aligned.fasta	Multiple sequence alignment of the EPM2A homologs
epm2a_tree.nwk	EPM2A phylogenetic tree (Newick format)
epm2a_tree.png	EPM2A tree image
tp53_homologs.fasta	Homologous sequences collected for TP53
tp53_aligned.fasta	Multiple sequence alignment of the TP53 homologs
tp53_tree.nwk	TP53 phylogenetic tree (Newick format)
tp53_tree.png	TP53 tree image

Workflow

1. Collect homologs: gather homologous sequences for the gene (FASTA).
2. Align: build a multiple sequence alignment of the homologs.
3. Build tree: infer a phylogenetic tree from the alignment and save it in Newick (.nwk) format.
4. Visualize: draw the tree and export it as a PNG image.

Tools used: add here (for example the alignment tool, tree-building method, and plotting library).

How to view the trees

• Open the .png files directly for a quick look.
• Open the .nwk files in a tree viewer such as FigTree, iTOL, or the ETE Toolkit / Biopython (Bio.Phylo).

from Bio import Phylo

tree = Phylo.read("tp53_tree.nwk", "newick")
Phylo.draw_ascii(tree)

Requirements (for the example above)

pip install biopython

Author

Hammad Memon, microbiologist learning bioinformatics (Python, Linux, R).