Talking about novel bioinformatic tools for DNA sequence submissions This Thursday, I held a conference talk at the 24th International Symposium on Biodiversity and Evolutionary Biology of the German Botanical Society. I introduced the participants to some of my newly developed tools for streamlining and automating the submssion of plant DNA barcoding sequences to public […]
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One-liner: Splitting multi-sequence FASTA into single-sequence FASTA
Quick, split it! There are one-liners that never get old. Here is another one of them. $ csplit multisequence.fasta /\>/ {*} && find . -size 0 -print0 |xargs -0 rm –
Workshop at the GfBS 2018
Talking about efficient data partitioning strategies Today, I held a workshop at the 19th annual meeting of the Gesellschaft für Biologische Systematik (GfBS). I introduced the participants to computational strategies to automate the selection of data partitioning schemes and nucleotide substitution models for phylogenomic datasets. […]
DCPS Day 2016
Today, different groups of the Dahlem Center of Plant Sciences met for their annual symposium, the DCPS Day 2016. It was a great symposium, and I enjoyed giving my presentation to this great set of research groups.
Excursion in Brandenburg
Yesterday, a few colleagues and I went on an excursion to the Döberitzer Heide, an anthropogenic heath in the state of Brandenburg. .
Lecture for high-schools students
Facilitating their transition to college As part of the Summer University 2016, a unique course by the Freie Universität Berlin that allows high-school students to attend college-type lectures, I organized a lecture session on plant evolution today. Lots of interested students and good questions afterwards!
Saving text elements as svg in R
A helpful note Saving text elements via the default svg-drivers of R (e.g., grDevices::svg, Cairo::CairoSVG) often results in the text being saved as paths instead of genuine text elements. Downstream svg-editors (such as Inkscape) may thus only allow you to move single letters but not edit them as text elements (which slashes the point of […]
Setting the default Python version in R
Easy if you know how. We are living in a time of interconnectivity, and barely a day goes by when I don’t use the scripting language R in a more or less intricate pipeline. Often I have R call out to the interpreted programming language Python or the system shell to run a third-party executable […]
Python version of rPython
R shell vs. RStudio NOTE: This blog post originally appeared on 12-Nov-2014 on the blog I kept when I was a postdoctoral researcher at the Ohio State University. I am reposting it here because several people have asked me about this very topic lately. On several occasions I have wondered which criterion the […]
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