The BiomolecularStructures package provides several Bioinformatics-related modules for Julia.

Some scripts to make your bioinformatics analyses reproducible and a bit easy 🤓

This pipeline automates the process of generating phylogenetic trees from sequence data, specifically designed for high-throughput and efficient analysis.

Modular Python bioinformatics library for genomic sequence analysis. Read preparation, assembly, homology search, clustering, multiple sequence alignment, and mapping as installable CLIs and importable modules.

A Python script that align SARS-CoV-2 genomes identifying and reporting pointwise variations.

🦇🦠🌳Study on detection of Brno loanvirus in Southern Russia

GUI and CLI workflow for phylogenetic tree construction, tanglegram comparison, and optional Foldseek protein-structure similarity.

Developed a bioinformatics workflow for the classification and functional characterization of the CAZy GH5 glycoside hydrolase family, a highly diverse enzyme family involved in carbohydrate metabolism.

This project performs an automated phylogenetic analysis of nucleotide sequences retrieved from NCBI. The pipeline includes sequence alignment, concatenation, phylogenetic inference (maximum likelihood, maximum parsimony, and Bayesian), and formatting for visualization.

Influenza A PB1 FASTA QC, alignment (MAFFT), and country-balanced sampling (R)

Automated maximum-likelihood phylogeny pipeline for viral families. Discovers species via NCBI Taxonomy, downloads from GenBank, aligns with MAFFT, builds trees with FastTree (broad) and IQ-TREE (refined), and annotates internal nodes by LCA. Supports multi-marker concatenation for large DNA virus families.

Pipeline to get a protein's residues conservation JSD scores

This repository contains a set of scripts and workflows designed to search for Respiratory Complex I (NADH Ubiquinone Oxidoreductase) subunits in prokaryotic genomes and proteomes.

This repository provides a reproducible pipeline for phylogenetic analysis using Nextflow, BLASTP, CD-HIT, MAFFT, trimAl, and IQ-TREE. The workflow supports automated BLAST search, clustering, alignment, trimming, and tree inference for protein.

Microbiome analysis pipeline with reference tutorial. This code was written in October 2024 to process rRNA marker gene data (16S and ITS) from rhizosphere soil samples.