Genome phylogeny using concatenated protein alignments made easy: quickCOAT

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I just wrote a small tool to help infer phylogeny from genome data. It’s called quickCOAT (quick Concatenated Ortholog Alignment Tree). You can download it from the quickCOAT Github page and try it out for yourself. quickCOAT works by taking a set of genomes (that is, protein sequences from each genome), using blastp to determine single-copy orthologs within that genome … Continue reading Genome phylogeny using concatenated protein alignments made easy: quickCOAT

Cable bacteria now have a name: genera Electrothrix and Electronema

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Cable bacteria were first discovered back in 2012, and although they’re quite narrowly defined phylogenetically, we’ve referred to them as “cable bacteria” rather than a proper scientific name. Names have now been proposed in a recent publication:   D. Trojan, L. Schreiber, JT Bjerg, A. Bøggild, T Yang, KU Kjeldsen, A Schramm, (2016). A taxonomic framework for cable … Continue reading Cable bacteria now have a name: genera Electrothrix and Electronema

New “tree of life” paper suggests a more rational way to define phyla

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Since we started cultivation-independent analysis of microbial DNA, there’s been an explosion in the number of phyla (or “candidate phyla”, “phylum-level groupings”, etc.). We’ve found a lot of microbes whose 16S rRNA genes, or other marker genes, do not cluster within established phyla, and therefore we create new phyla to accommodate them. This creates a … Continue reading New “tree of life” paper suggests a more rational way to define phyla

Dynamic plots could be really useful for science – sediment cell count/age/TOC example

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Once upon a time, scientific papers used to be available on real paper, and only on real paper. I’m lucky enough to have started doing science in the era of digital publication, but recently I’ve started to suspect that we’re vastly under-utilising the potential of digital publication. Our papers are still PDFs, i.e. static on-screen … Continue reading Dynamic plots could be really useful for science – sediment cell count/age/TOC example

Finally, a reductive dehalogenase in a marine deep-subsurface Chloroflexi genome

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There are many well characterized organohalide-respiring bacteria from the phylum Chloroflexi, especially from within the class Dehalococcoidia, like Dehalococcoides mccartyi. The question has always been what context this trait of obligate organohalide respiration (and the genes encoding the necessary reductive dehalogenases) evolved in – we’ve often looked to ocean sediment, as the ocean is where … Continue reading Finally, a reductive dehalogenase in a marine deep-subsurface Chloroflexi genome

Why I don’t think I should submit preprints

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The idea of posting “preprints”, or un-reviewed, unpublished manuscripts ahead of normal review and publication, has been gaining popularity recently (although it’s been around for a long time in other fields, like physics). Especially now that we have a preprint server dedicated to biology, there’s people saying that publishing preprints can help science be disseminated … Continue reading Why I don’t think I should submit preprints