Category Archives: bioinformatics

What is DAS? A new tool to recover genomes from metagenomes

Posted on 8 Jun, 2018 by Kelle Freel

There are a lot of data out there, and if you haven’t already noticed the ‘omics train has steadily stayed its path through the fruitful (but challenging) world of metagenomics. Metagenomics offers the chance to unravel complex microbial communities without … Continue reading →

Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, next generation sequencing | Tagged , , , | Leave a comment

La vie en rouge … l'algue rouge

Posted on 4 Jun, 2018 by Stacy Krueger-Hadfield

Best laid plans of a #NewPI … what happens to them? Well, they often get triaged for more urgent things that were triaged earlier for more urgent things that were also triaged even earlier for more urgent things … and … Continue reading →

Posted in adaptation, bioinformatics, blogging, conferences, evolution, fieldwork, haploid-diploid, mating system, natural history, population genetics, selection | Tagged , , , , , , , , | Leave a comment

Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies

Posted on 10 Apr, 2018 by Katharine Coykendall

Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading →

Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics | Tagged , , , , , , , , , , | 1 Comment

Found in translation: The evolutionary history of RNA viruses in vertebrates

Posted on 6 Apr, 2018 by Kelle Freel

I have to admit, viruses aren’t normally my thing, but this is pretty darn cool. In a study out by Shi and colleagues this week, researchers identified 214 new viruses that, as the authors so succinctly state, reveal “diverse virus-host … Continue reading →

Posted in bioinformatics, Coevolution, evolution, transcriptomics | Tagged , , | Leave a comment

Major new microbial groups expand diversity and alter our understanding of the tree of life

Posted on 18 Mar, 2018 by Laetitia Wilkins

I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading →

Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics | Tagged , , , , , , , | 1 Comment

Exploring the genomic diversity of tubeworm endosymbionts

Posted on 1 Feb, 2018 by Kelle Freel

Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how … Continue reading →

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Retrieving a million sequences and avoiding primer bias, a new method that might have it all

Posted on 19 Jan, 2018 by Kelle Freel

We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA … Continue reading →

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Molecular ecology, the flowchart

Posted on 2 Jan, 2018 by Jeremy Yoder

Update: You can now buy a poster print of the Flowchart, with proceeds going to support The Molecular Ecologist! Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for … Continue reading →

Posted in association genetics, bioinformatics, genomics, howto, infographic, linkage mapping, next generation sequencing, phylogenetics, phylogeography, population genetics, selection | 2 Comments

Visualize your genome assemblies

Posted on 18 Dec, 2017 by Elin Videvall

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily), is a program that creates visualisations of sequence assemblies that you can interact with. When assembling a genome with your favorite assembler, you are usually building graphs, from which … Continue reading →

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Diving deep: Exploring microbial communities under the seafloor

Posted on 7 Dec, 2017 by Kelle Freel

As we all sat staring at three large monitors in the front of the room, the remotely operated vehicle (ROV) Jason hung on to a borehole observatory with one hydraulic arm as the other arm plugged our sampling equipment into … Continue reading →

Posted in bioinformatics, community ecology, fieldwork, genomics, metagenomics, microbiology, transcriptomics | Tagged , , , | Leave a comment