snpick is a fast and memory-efficient Rust-based SNP extraction tool designed to handle large genomic alignments with minimal RAM usage and high-speed performance.

This repository provides a comprehensive tutorial for phylogenetic analysis, covering data collection, sequence alignment, tree construction, and interpretation. It runs on AWS SageMaker using Jupyter notebooks and includes tools like MAFFT, Nextclade, and IQ-TREE.

Complete pipeline that mirrors the manuscript: reference based assembly with depth masking, de novo checks, phylogeny with configurable models including ModelFinder, and targeted mutation analysis for G and F versus NC_038235.1 and NC_001781.1. Includes CI and environment files for easy setup.

This repository contains some phylogenetic trees I have done for practical purposes.

A Nextflow pipeline to generate a phylogenetic tree from SKA alignment