Bioinformatics

For my courses ofwork in Linux command line not only for MetaCentrum and with molecular data in R I provide VirtualBox image, which allows to run complete desktop Linux (in this case openSUSE Leap) with all preinstalled applications needed for both courses. It's easy way how to get fully working Linux to play with. It requires at least bit powerful notebook, e.g. at least quad-core with at least 8 GB RAM, but more is better.

Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome.

Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.

Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested.

Intensive 4-days (5^th day is not compulsory, but is open for any discussion, if there would be interest) course to learn all theory about HybSeq and practically learn how to analyze HybSeq data, how to solve all problems, and how to evaluate differences among gene trees. Important part is enough time to discuss everything, including practical problems and projects of individual participants.

Poster presented at Botany 2018 conference of the Botanical Society of America titled Hunting the treasure of Cape Oxalis diversity (Zeisek, Oberlander, Dreyer, Schmickl, Schneeweiss):

Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in non-model organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region.