Interested in microbial ecology and evolution.
Peer reviewed + preprint studies I have contributed to can be found on my Google Scholar ๐จโ๐
๐ = on Bioconda; ๐ = on Docker Hub; ๐ฅง = on PyPi
- zol (& fai): ๐ ๐ suite for evolutionary and functional analysis of gene clusters (co-located sets of genes).
- skDER (& CiDDER): ๐ ๐ programs for genomic dereplication using ANI and pan-genome saturation approximation.
- lsaBGC-Pan: ๐ ๐ suite/workflow for pan-BGC-ome analyses.
- codoff: ๐๐ฅง 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: ๐ 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.