Category Archives: bioinformatics

Music to an amniote's ears, an "accordion" model of genome size evolution

Posted on 10 Feb, 2017 by Kelle Freel

How did we get where we are? Genetically speaking, that is. A few posts ago, that whole genotype-phenotype question was discussed, how do genomes make plants and animals (and don’t forget the microbes!) look and act how they do. Another … Continue reading →

Posted in adaptation, bioinformatics, evolution, genomics | Tagged , , , | 2 Comments

Phylogenetic trees in R using ggtree

Posted on 8 Feb, 2017 by Elin Videvall

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 →

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

Handling microbial contamination in NGS data

Posted on 6 Jan, 2017 by Ethan Linck

Until recently, I had given little thought to the potential for unwanted microbial contamination in high throughput sequence data. I suspect that if you’re a molecular ecologist who doesn’t primarily study microbes or work with ancient DNA, you’re in a … Continue reading →

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

Unbalanced population sampling and STRUCTURE

Posted on 5 Jan, 2017 by Arun Sethuraman

The utility and intuition offered by the program STRUCTURE, and more generally, the ‘admixture’ model of Pritchard et al. (2000) are unquestioned – with tens of thousands of citations, it retains its lead among the most popular population genetics software. … Continue reading →

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

There are more microbes than meet the eye: exploring the genomic diversity in an aquifer

Posted on 8 Nov, 2016 by Kelle Freel

First: it’s Tuesday, November 8th, 2016 – before you even think about putting your feet up and reading this post, I hope you’ve managed to wrangle yourself one of those highly prized “I voted” stickers. Now, on to more microbial … Continue reading →

Posted in bioinformatics, community ecology, metagenomics, microbiology, next generation sequencing | Tagged , , | 1 Comment

Making ecology “count”: a review of the why and how of molecular ecology  

Posted on 25 Oct, 2016 by Kelle Freel

It’s likely that everyone has been asked by either a friend or family member “What do you do?” Which, depending on what level of detail you shoot for, might be relatively straight forward. The follow-up question, however, can be a … Continue reading →

Posted in bioinformatics, community, community ecology, metagenomics | Tagged , , , | 1 Comment

When your programming may be inadequate to the task: new options for metagenome analysis

Posted on 9 Sep, 2016 by Kelle Freel

There’s a lot of data in the form of metagenomes out there, and picking apart those mountains of data to uncover meaningful results is difficult. Recently, we received a suggestion from a reader to discuss a recent program (CLARK-S) developed … Continue reading →

Posted in bioinformatics, community ecology, metagenomics, methods | Tagged , , , , , | Leave a comment

Is equilibrium out of reach or are there some sneaky bouts of sex?

Posted on 30 Aug, 2016 by Stacy Krueger-Hadfield

Reproductive systems impact the evolution of genetic diversity at the population level. Yet, we don’t know a lot about organisms that are partially clonal, despite the large component of biodiversity that dabbles in asexual reproduction to varying degrees. Clonal dynamics are … Continue reading →

Posted in bioinformatics, evolution, genomics, natural history, next generation sequencing, theory | Tagged , , , | 1 Comment

The trouble with PCR duplicates

Posted on 25 Aug, 2016 by Reid Brennan

The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading →

Posted in bioinformatics, genomics, methods, next generation sequencing | Tagged , , , | 6 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