Category Archives: software

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

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

RedditDiggMendeleyPocketShare and Enjoy
Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, software | Tagged , , , | Leave a comment

Poorly updated databases will affect your results

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

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 , | Leave a comment

On Integrative Species Delimitation…

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 | Leave a comment

A new (quantitative!) method for comparative phylogeography

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

Battle of the Text Editors

Whether you’re a coding master or a total technophobe, a good text editor is a must-have for the molecular ecology toolkit. Text editors are great for managing code, formatting input files, or jotting notes. But with so many different text … Continue reading

Posted in bioinformatics, software | Tagged , , | 2 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

Posted in bioinformatics, howto, R, software | Tagged , | Leave a comment