Category Archives: software

Video Tutorial: editing R plots in Adobe Illustrator

Posted on 20 Oct, 2016 by Katie Everson

Adobe Illustrator is a powerful tool for creating and editing figures; unfortunately, it’s also really intimidating. So today at The Molecular Ecologist we’re trying something a little different: a screen-capture video tutorial about using Adobe Illustrator to enhance and edit plots … Continue reading →

Posted in howto, R | Tagged , , , , , , , , | 3 Comments

A Primer on the Great BAMM Controversy

Posted on 26 Aug, 2016 by Ethan Linck

Update, 26 August 2016, 2:30PM. A number of readers brought my attention to a series of blog posts by Moore et al. responding to Rabosky’s rebuttal of their published critique of BAMM. I’ve included links to the posts and summarized their … Continue reading →

Posted in evolution, phylogenetics, software, speciation | Tagged , , , , , , | 5 Comments

On (mis)interpreting STRUCTURE/ADMIXTURE results

Posted on 5 Aug, 2016 by Arun Sethuraman

STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading →

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , , , | 1 Comment

STITCH, in time, could save a lot of array design

Posted on 12 Jul, 2016 by Jeremy Yoder

A new algorithm for processing DNA sequence data, STITCH, could lower costs for studies of genetic variation within species by reconstructing, or “imputing”, the sequences of individual samples within a larger dataset. The ongoing proliferation of high-throughput (or, ugh, “next … Continue reading →

Posted in association genetics, bioinformatics, genomics, methods, next generation sequencing, software | Tagged | Leave a comment

Making Maps in R, volume 2: ggplots

Posted on 1 Jul, 2016 by Jeremy Yoder

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 →

Posted in howto, R, software | Tagged , | 7 Comments

Data, data everywhere and another tool to use: Taxonomer, a web-tool for metagenomics data analysis

Posted on 26 May, 2016 by Kelle Freel

Because sequencing. With all the affordable genome and metagenome sequencing available, we’ve reached an unprecedented point at which we can profile microbial communities more accurately than ever before. For this reason, it’s essential to develop efficient methods for data analysis. … Continue reading →

Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, software | Tagged , , , | 1 Comment

Poorly updated databases will affect your results

Posted on 24 May, 2016 by Elin Videvall

If you’re anything like me, your research is heavily dependent on the many wonderful database resources available online. NCBI, UniProtKB, Ensembl, Swiss-Prot, EMBL-EBI, and many other sites and organizations offer highly useful (and often curated) molecular information. Can you imagine … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing, software | Tagged , , , , , | Leave a comment

Docker: making our bioinformatics easier and more reproducible

Posted on 13 May, 2016 by Jeremy Yoder

This is a guest post by Alicia Mastretta-Yanes, a CONACYT Research Fellow assigned to CONABIO, Mexico. Her research uses molecular ecology and genomic tools to examine the effect of changes on species distributions due to historical climate fluctuations as well … Continue reading →

Posted in bioinformatics, software | Tagged , | 1 Comment

On Integrative Species Delimitation…

Posted on 9 May, 2016 by Bryan McLean

Accurate delimitation of species is a fundamental first step that underlies much of what we do in biology. But this can prove challenging in many situations. Why? Let me count the ways. Incomplete lineage sorting, hybridization, morphological conservatism, and niche … Continue reading →

Posted in evolution, methods, phylogeography, population genetics, software, species delimitation | 1 Comment

A new (quantitative!) method for comparative phylogeography

Posted on 4 May, 2016 by Katie Everson

Comparative phylogeographic studies usually involve a) documenting a phylogeographic pattern and b) recognizing that the same pattern is congruent in multiple species. But what if species histories are only sortof congruent? Perhaps they share one major splitting event but not later … Continue reading →

Posted in Coevolution, phylogeography, plants, software | Tagged , | 5 Comments