Lichenologist · Computational Biologist · University of Graz

I study the evolution, ecology and genomics of lichen-forming fungi. My work combines classical lichenology - fieldwork, taxonomy, microscopy and ecology - with phylogenetics, comparative genomics, transcriptomics, reproducible workflows and open-source teaching material.

I am particularly interested in lichen symbioses, fungal adaptation, phylogenomic inference, phylogenetic comparative methods and the development of practical tools that make biodiversity and genomics workflows easier to implement, teach and reproduce.

• phylociraptor - rapid phylogenomic tree calculator. a reproducible framework for phylogenomic inference.
• annocomba - automated genome annotation pipeline combining MAKER and funannotate with Singularity and Snakemake.
• binner - combine multiple metagenome filtering/binning programs using Docker containers.
• concat - Python script for building concatenated FASTA matrices from single-locus alignments.
• correlate - R package for character correlation analyses with phylogenetic trees.
• iqtreeGUI - graphical user interface for IQ-TREE.
• quickblast - small shell utility for quickly creating BLAST databases and querying sequences.
• alignment-viz - scripts for processing and visualizing sequence alignments.
• TEid - Python project related to the identification of Transposable Elements.

• tlcid - visual thin layer chromatography substance identification for lichens.
• tlcid-database - companion database/resources for TLCid.

• gbif-sdm-practical - introduction to working with GBIF data and species distribution models.
• bioinformatics-and-genomics - course material and syllabus for the Bioinformatics and Genomics module at the University of Graz.
• reproducibility-workshop - course material for reproducibility in bioinformatics.
• phylociraptor-workshop - introduction to working with phylociraptor.
• lichen_genomics - course material for the workshop on lichen genomics in Graz in 2017.
• transcriptomics-intro - introductory transcriptomics teaching material.
• linux-intro - introductory Linux teaching material.

• dockerfiles - collection of Dockerfiles for bioinformatics, genomics and phylogenetics containers.
• ct - tool to list, search and retrieve commands for my container collections.
• rstudio-docker - RStudio Docker setup.
• funannotate-docker - Docker container for the funannotate genome annotation pipeline.
• jupyterhub-singularity - JupyterHub/Singularity infrastructure work.
• immediate-submit - immediate-submit helper script used in various Snakemake HPC pipelines.
• LFS-cazy-comparative - code for comparative genome analyses from Resl et al. 2022, Nature Communications.
• smsi-funannotate - Snakemake/Singularity pipeline for funannotate workflows.
• saccharis-docker - Docker setup for SACCHARIS/CAZyme-oriented annotation workflows.
• smsi-minibarcoding - Scripts related to MinION barcoding.

• nimbio - Nim-based bioinformatics experiments.
• genomics - scripts used in genomic data analysis workflows.
• phylo-scripts - Python scripts for phylogenetic analyses (no longer developed).

• reslp.github.io - personal academic website.
• blog - blog source/material.
• homestack - Raspberry Pi/home infrastructure notes and setup.