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

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

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.

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

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

A bioinformatics pipeline for the systematic identification and evolutionary analysis of MADS-box gene families. Utilizes advanced genomic screening to trace plant developmental genetics and evolutionary lineages.

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

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

Influenza antiviral resistance interpretation pipeline using amino acid sequences and WHO mutation rules.

Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.

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.

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

Codon-aware phylogenetic pipeline with Snakemake

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.

Representative sequence selection for large bioinformatics datasets

Pipeline to get a protein's residues conservation JSD scores

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.

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.

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.

Computational workflow for comparative genomic analysis, SSR identification, conserved marker validation and gene mapping in Nipah virus genomes