Inferring a ML tree with 12000 (or more) virus genomes

Somebody on the RAxML group posted this as a bold question, asking for tips how to speed up the analysis. Since I recently looked at virus genomes (infamous SARS group) myself, I have some ideas for this.

Now that RAxML includes all models – a practical tip

The new, faster and (meanwhile) very option-rich version of RAxML, RAxML-NG provides the full plethora of nucleotide substitution models, which can be confusing to the normal user. Hence, a practical tip based on my experiences with very different sets of nucleotide data (and from very different organisms).

Why I never published a "total evidence" tree

Triggered by a support question on the RAxML google group, I pondered the question whether it makes sense (anymore) to use the total evidence approach to place fossils.

The Easter Egg featuring Earth, live

For this Eastern, I'll advertise something colourful to turn our eyes back from ourselves to the planet we inhabit: a live simulation/representation of Earth's dynamic surface and atmosphere.

Scientists = surveyed customers? Bite me.

Science is good business. Especially since the public hand pays for most of it, via salaries and research grants, library conscriptions ensuring high profits for science publishers, providing infrastructure and – at least in western welfare states – students. An invitation for a customer survey.

Surviving parsimonists: just tree-naive or tree-blindfolded?

A generation ago, an epic battle took place, largely unnoticed outside mathematical and biological sciences: the Phylogenetic Wars. By the mid-1990s, the war was over and probabilistic methods for tree-inference replaced traditional parsimony. But there is a small, quite dusty realm that still pretends nothing happened: palaeontology. A long read about undervalued data and stubborn old white men.

Lernen mit Lindner – die Geometrie der Mitte

Nach dem PR-Fiasko in Thüringen, macht die FDP wieder ganz auf Mitte. Zeit für eine paar Bildchen.

Tempolimit? Nein, danke! Realsatire? Bitte mehr!

Dank Trumpelchen, des First Toddlers of the United States, Bojos Mojo und ähnlicher Gestalten ist es schwierig geworden, Satire und Realpolitik auseinanderzuhalten. Und die CSU ist wie immer vorne mit dabei bei dem neuen Trend.

And the laughter dies

Germans are generally not known for their sense of humour (although this is a gross-generalisation, German humour can be quite diverse, and differs from region to region). But there are exceptions. However, these days, it's the audience who gets at you.

A Wikipedia list everyone should know

Wikipedia has changed the world how we access knowledge. And despite recent (and fair) criticism, it's still an invaluable social project because it provides easy entry portals and an enormous wealth of quick-to-access data. Approaching Christmas, the Feast of Love and Peace, I'd like to point towards a Wikipedia page dealing with something, we tend to quickly forget about: Wikipedia's List of ongoing armed conflicts.

If you haven't done yet: sign up on The Cost of Knowledge

I got an invitation to review a paper for Molecular Phylogenetics and Evolution. Naturally, I declined to review. And you should, too. Always. Because it's published by Elsevier.

Fare well, Brittania!

The Bojo worked, Her Majesty finally will be able to appoint a proper English government with a fine majority. An add-on to Brittania, sail away! from October this year.

Wer will die 5%

Es wird haarig im Osten für die ehemalige Allmachtspartei CDU, die SPD in Brandenburg hat rechtzeitig rechtsgeblinkt. Gereicht hat es trotzdem nicht. Ein Kommentar zur 5%-Hürde, den vielbeschworenen stabilen Mehrheiten. Mit Grafiken natürlich.

Knackt endlich die Haselnuß!

Verfolgt man die z.T. etwas hysterischen Reaktionen auf Twitter zum Schmusekurs der Thüringer CDU mit den Schmuddelkindern der AfD (die in Thüringen besonders schmuddelig sind), fällt oft der Gedanke von "Wehret den Anfängen!". Ein Kommentar zur braunen Welle, die nun auch Deutschland erreicht hat.

Thüringen 2019: Kein weiteres Afghanistan, sondern skandinavische Verhältnisse

Thüringen hat gewählt. Wie es aussieht, eine Minderheitsregierung. Eine Nachlese zu den Landtagswahlen im Osten (wie gewohnt, mit Wahl-O-Mat Netz).

Brittania sail away!

I sympathise with our former fellow Europeans, the British. But whether we like it or not, their electorate wants to leave the EU, no matter how stupid it's going to be. A short post on non-representative democracies.

Would you like to have your own edited paper collection?

One of the biggest problems in peer-reviewed science is editor-bias. So, my answer to Frontiers in Plant Science's nice invitation, even if I would still be in professional science, can only be no!

When dating is futile – plastome-based chronograms for oaks

With most-versatile programmes like BEAST at hand, everyone can do a molecular dating. Which makes it even more important that editors and peers check the priors and reasoning behind it. And always should make sure a palaeobotanist (or at least, a palaeogeographer) is one of the peers.

Soft phishing, and why anyone should know GoogleScholar

I still have a university e-mail address, for fiscal reasons. Hence, I still get what we call in German Initiativbewerbungen, not solicited applications for joining my working group (I never had one) from people in countries not as happy as Austria. And the one or other phishing mail.

Why you never should do a single-species plastid analysis of oaks

The fragmentation of science makes it more and more difficult to keep up scientific standards. Editors struggle harder and harder to find peers who have the knowledge and time to properly review the papers of others. Hence, in even relatively transparent peer-reviewed journals, the same errors are endlessly repeated. For instance: phylogenetic/-biogeographic studies on Chinese oaks using plastid data.