Author: Siva Subramanian Ayeraselvan
Date: June 2025
This repository contains the scripts, data files, and documentation associated with my Master's thesis in Genomics. The project focuses on analyzing genomic datasets to address biological questions related to:
- Adaptation
- Niche modeling
- Conservation genomics
The analyses combine next-generation sequencing (NGS) data processing with advanced statistical and ecological modeling.
├── NGS_genomic_analysis
├── GEMMA/ # GWAS / GEA genome environmental association scripts
│ └── GEA_scripts/
├── mar/ # mutation area relationship - conservation genomics
├── maxent_manual/ # detailed overview to perform maxent
├── gradient_forest/ # GF analysis i performed
└── README.md # This file
The following methods and analyses are included:
- Genome-Environment Associations using GEMMA
- Species Distribution Modeling with MaxEnt
- Gradient Forest analysis for adaptive genomic variation
- Mutation-Area Relationship (MAR) analysis for conservation applications
- Python >= 3.8
- R >= 4.2
- GEMMA
- maxENT
- Gradient Forest (R package)
- BEDTools
- VCFtools
- Samtools
- BCFtools