Tools for Data Analysis and Biological Discovery

This page presents a selected set of bioinformatic tools that I have developed or contributed to. These tools span a range of biological topics and are designed to support researchers in analysing their own data and addressing their research questions. The focus is on accessibility and broader applicability across the scientific community.

Please note that this is only a representative selection. For a more comprehensive overview of my work and related tools, you are welcome to explore the following platforms:

I am committed to supporting open, reproducible, and transparent research. The tools listed here reflect that commitment and are intended to empower researchers with reliable and reusable resources.

  • DOGMA

    DOGMA A tool for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains.
    Implementation: Python
    User Interface: CLI, Webserver
    Linked Publications: 📄 📄
    Availability: 🏠 GitLab 🌐
    modern version with additional features in development...stay tuned!

  • DomRates

    DomRates A tool for infering domain rearrangement events and their rates across phylogenetic trees.
    Implementation: C++
    User Interface: CLI
    Linked Publications: 📄 📄
    Availability: 🏠 GitLab

  • DeNoFo

    DeNoFo A file format and toolkit for standardized, comparable de novo gene annotation.
    Implementation: Python
    User Interface: GUI, CLI
    Linked Publications: 📄 📄
    Availability: 🏠 GitHub 🐍

  • DESWOMAN

    DESWOMAN A tool for automatic detection of de novo gene precursors and analysis of their mutations based on transcriptome data.
    Contribution: Python packaging and dockerizing, consulting
    Implementation: Python
    User Interface: GUI, CLI
    Linked Publications: 📄
    Availability: GitHub 🐳

  • GEvol comparative genomics pipeline

    GEvol pipeline A Snakemake-based bioinformatic workflow designed to streamline the evolutionary analyses in comparative proteomics.
    Implementation: Snakemake
    User Interface: CLI
    Linked Publications: coming soon...
    Availability: in development

  • DomTree

    DomTree A Deep Learning-based tool to reconstruct phylogenetic trees based on whole proteome information through protein domains.
    Implementation: Python, C++
    User Interface: CLI
    Linked Publications: Chapter 5 in: 📄 Availability: in development
    A new improved version, addressing the described problems and shortcomings in the linked publication is currently in development.