Welcome to Eco-Phylo Insights, a computational biology project focused on uncovering evolutionary relationships between turtles, lizards, crocodiles and birds through sequence alignment and phylogenetic tree construction.
This repository is part of my personal portfolio and showcases my ability to work with genetic data, implement distance models (like Jukes-Cantor and Kimura), and visualize evolutionary patterns using Python.
- 🐢 Compares multiple vertebrate species (reptiles and birds)
- 🧬 Implements Jukes-Cantor and Kimura 2-Parameter models to calculate evolutionary distances
- 🌱 Constructs phylogenetic trees using UPGMA and Neighbor-Joining
- 📊 Includes clear visualizations of distance matrices and resulting trees
- Using comparing methods like Robinson-Foulds distance, Least-squares distance, Quartet distance.
- ⚙️ Built entirely in Python, in an interactive Jupyter Notebook
Tree generated with Clustal Alignment and Kimura distances using the UPGMA method.
Tree generated with Clustal Alignment and Jukes-Cantor distances using the Neighbor-Joining method.
- Data Import & Preprocessing: FASTA sequences of turtles, lizards, and birds.
- Multiple Sequence Alignment: Using MUSCLE or Biopython tools.
- Distance Matrix Generation:
- Jukes-Cantor model (assumes equal mutation probability)
- Kimura 2-Parameter model (accounts for transitions and transversions)
- Phylogenetic Tree Construction: Using UPGMA and Neighbor-Joining algorithms.
- Custom implementation of both Jukes-Cantor and Kimura models
- Clear and reusable functions for distance matrix creation
- Insightful visual comparison between models
- Integration with tree-building methods to show practical impact of model choice
- Python 3.x
- Jupyter Notebook
- Biopython
- scikit-bio
- matplotlib
- ete3 (for tree rendering)
Ana Laura
LinkedIn]
MIT License — feel free to use, cite, and build upon this project.