mafft

Reference-based consensus creation

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

Auditable agent skill for resolving protein queries, selecting references, and planning reproducible phylogenetic trees.

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.

DesignLab — conservation-aware PCR/qPCR primer design: NCBI search, MAFFT alignment, conserved-block Primer3 design and in-silico validation, with every binding site visualised

Representative sequence selection for large bioinformatics datasets

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.

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

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

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.

🦇🦠🌳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.

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.

Codon-aware phylogenetic pipeline with Snakemake

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

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.

Python toolkit for interpretable influenza HA mutation-tree analysis

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.