Michael Grünstäudl (Gruenstaeudl), PhD

Postdoctoral Researcher at the Freie Universität Berlin

Archiv der Kategorie 'Allgemein'

Talk and workshop at Botany 2021

Summer time is conference time. As part of the joint conference (“Botany 2021 – Virtual!“) of several North American botanical and mycological societies, I am giving two scientific presentations: a regular talk in the topic section on comparative genomics and a workshop presentation. The workshop has been recorded and can be viewed online here (login […]

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Simple indel coding “for to go”

The process of coding insertions and deletions in a multi-species DNA alignment such that the presence of these indels can be used as additional information in a phylogenetic investigation is typically referred to as “indel coding”. Multiple indel coding schemes exist, with a scheme proposed by Simmons and Ochoterena (2000; often referred to as “simple […]

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New Paper – An R package for visualizing plastome coverage depth

Visualizing the depth I just published a new paper on an R package that assists users in visualizing the coverage depth of a plastid genome in relation to its circular, quadripartite genome structure. Co-author of the software is an undergraduate student, who (as part of his bachelor thesis) designed the visualization engine of the software.

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New paper – A Python package for large-scale DNA sequence submissions

Large-scale DNA sequence submissions to ENA I just published a new paper on a Python package to submit large DNA sequence datasets to ENA. Special thanks go out to a master’s student of mine who was fantastic in assisting me with testing and debugging the software!

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Teaching in Spring 2019

Teaching. “Usus artium magister, dicendo dicere discunt.” (Eucharium Eyering, Copiae Proverbium)                

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Commandline search interface for ENA

Digging through ENA records. By using the Python library enasearch, which provides a Python-based interaction with ENA’s API, commandline searches of the ENA databases have become a delight. Take, for example, the aim to infer the number of individual accessions of the common plant DNA barcoding marker trnK-matK that have become available over the course […]

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Botanical field trip in the Carinthian Alps

Alpine plants in the mist An alpine field trip in late September can mean cold temperatures and lots of foggy weather. Interesting plants abound nonetheless.

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Talk at evolutionary plant biology conference

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 —

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Teaching in spring 2018 – Part II

                           

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