Stay up to date
Subscribe via email
Latest comments
Archives by month
Contributors
Editor
Founding editor
Contributing writers
- Reid Brennan — @reidbrennan
- Melissa DeBiasse — @MelissaDeBiasse
- Rob Denton — @RD_Denton
- Katie Everson — @km_everson
- Kelle Freel — @KC_freel
- Kim Gilbert — @kj_gilbert
- Stacy Krueger-Hadfield — @quooddy
- Ethan Linck — @ ethanblinck
- Bryan McLean — @_RealMcLean
- Patrícia Pečnerová — @PataPecnerova
- Arun Sethuraman — @arunsethuraman
- Noah Snyder-Mackler — @hesheatingup
- Kathryn Turner — @ktinvasion
- Alex Twyford — @Alex_Twyford
- Elin Videvall — @ElinVidevall
- Laetitia Wilkins — @M_helvetiae
Alumni
Meta
Category Archives: howto
Making Maps in R, volume 2: ggplots
The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the … Continue reading
10 simple rules for designing a scientific poster
Conference season is upon us! Around the world, thousands of scientists face a daunting task: designing a scientific poster. It should be sleek, yet informative; eye-catching, yet professional; and most of all it should attract the attention of your future … Continue reading
How to make the most out of your phylogenetic study
Phylogenetic studies are crucial for ecology and evolution. However, their usefulness for comparative biology or meta-analyses can vary considerably. Especially the inclusion of unidentified species (“Balanus sp.”) obstructs their use in comparative studies. How can I attach life history or morphological data … Continue reading
Posted in data archiving, evolution, howto, phylogenetics, Uncategorized
Leave a comment
Using R to mine species data
Many of us generate more data than we know what to do with (speaking of which: keep an eye out for the 2016 NGS Field Guide, coming soon!), so it’s easy to forget about the piles of data already at our fingertips. Research potential is … Continue reading
The 2016 Next-Generation Sequencing Field Guide Preview: Zombie Systems and New Hope
After a year of minimal activity, we finally have some significant changes in Next Gen Land. In the 2016 update of the NGS Field Guide, I will continue to give my overall interpretation about the various instruments, but with less … Continue reading
Posted in genomics, howto, methods, RNAseq, transcriptomics
Tagged Illumina, Ion Torrent, NGS Field Guide, PacBio
8 Comments
Geographical Heat Maps in R
I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading
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
Posted in howto, methods, phylogenetics, R, software
Tagged ape, distance matrices, maximum likelihood, nucleotide evolution, parsimony, phangorn, phylogenetics, R
3 Comments
2D Posterior Density Plots in R
I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading
Posted in bioinformatics, howto, population genetics, R, software
Tagged data visualization, genomics, population genetics, R
1 Comment
On false positives in Isolation with Migration analyses
The IM suite of tools (IM, IMa, IMa2, IMa2p, etc.) are used widely by molecular ecologists at large for the analyses and estimation of ancestral demography under an Isolation with Migration (IM) model. However, these tools come with fundamental assumptions … Continue reading
Posted in evolution, genomics, howto, IMa2, methods, Molecular Ecology views, natural history, population genetics, software, theory
Tagged Evolution, gene flow, genomics, IM, isolation with migration, methods, migration, population genetics
1 Comment
PCA of multilocus genotypes in R
An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading
Posted in bioinformatics, genomics, howto, population genetics, R, software
Tagged data visualization, Homo sapiens, R
6 Comments