Tag Archives: phylogenetics

Metabarcoding for every body, every habitat, every time

The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading

Share
Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R | Tagged , , , , , , | Leave a comment

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

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

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

Phylogenetic trees in R using ggtree

Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has … Continue reading

Share
Posted in bioinformatics, howto, phylogenetics, R | Tagged , , , | 2 Comments

Quick and dirty tree building in R

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading

Share
Posted in howto, methods, phylogenetics, R, software | Tagged , , , , , , , | 3 Comments

Grasping gorgonians

A recent issue of Heredity focused on the brave new world of environmental genomics. After highlighting the special issue, I started chatting to one of the contributors, Eric Pante and became interested in his work on gorgonians. Eric and his co-authors explored the … Continue reading

Share
Posted in bioinformatics, Coevolution, evolution, genomics, mutation, phylogenetics | Tagged , , , , , | 1 Comment

#EntSoc14, a quick review

I have had a wonderful time at my first big bug conference – the annual meeting of the Entomological Society of America, at the Oregon Convention Center in Portland. Amid secretive (or not so secretive) break-out sessions to Voodoo Doughnuts, … Continue reading

Share
Posted in conferences, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

A tale of two Dryad submissions

As it happens, the last two scientific papers I’ve had accepted for publication are also the first two papers for which my first-authorial duties included some substantial journal-mandated archiving of supporting data (beyond uploading a handful of DNA sequences to … Continue reading

Share
Posted in data archiving, peer review | Tagged , , , , , | 8 Comments