Interested in microbial ecology and evolution.

Peer reviewed + preprint studies I have contributed to can be found on my Google Scholar 👨‍🎓

🐍 = on Bioconda; 🐋 = on Docker Hub; 🥧 = on PyPi

• zol (& fai): 🐍 🐋 suite for evolutionary and functional analysis of gene clusters (co-located sets of genes).
• skDER (& CiDDER): 🐍 🐋 programs for genomic dereplication using ANI and pan-genome saturation approximation.
• lsaBGC-Pan: 🐍 🐋 suite/workflow for pan-BGC-ome analyses.
• codoff: 🐍🥧 program to statistically assess differences in codon usage between a focal region and the background genome.
• psaps: program to assess pangenome expansion rate differences of clades by standardizing them using phylogenetic breadth.

• lsaBGC: 🐋 suite for genomic and metagenomic mining of micro-diversity in BGCs and general evolutionary analysis.
• ConSequences: programs to find long (>10 kb) contiguous and conserved (> 99% identity) segments across genomes associated with specific geographic locations.
• seQouia: framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial (meta-)genomic sequencing datasets.
• AncestralGeneRator: programs to simplify ancestral state reconstruction of ortholog group copy counts across phylogeies.
• PerMutation: Programs for statistical determination of essential and conditionally essential genes from E. faecalis TnSeq datasets.