Category Archives: bioinformatics

RADseq and missing data: some considerations

Posted on 10 May, 2016 by Ethan Linck

Unlike Sanger sequencing, where loci are directly targeted for each individual and sequencing errors are relatively rare, massively multilocus datasets from next generation sequencing platforms are characterized by large amounts of missing data. This is particularly true for restriction digest … Continue reading →

Posted in bioinformatics, genomics, methods, Molecular Ecology, the journal, next generation sequencing, phylogenetics, population genetics, theory | Tagged , , , | 6 Comments

Sweeps and Demographic Inference

Posted on 25 Apr, 2016 by Arun Sethuraman

Population genetics presents us with numerous conundrums – several of which have to do with how the same genomic disposition can be “reached” over evolutionary time with multiple alternate demographic or selective processes. I have discussed several of these issues … Continue reading →

Posted in bioinformatics, evolution, genomics, population genetics, selection, theory | Tagged , , , | Leave a comment

New branches on the tree of life

Posted on 12 Apr, 2016 by Kelle Freel

(Trees from Darwin (1837), Haeckel (1866), and Woese (1990)) We’ve come quite a long way since Darwin sketched out his tree in 1837 connecting, with branch tips representing animals and microbes currently in existence and branches and trunks their ancestors. … Continue reading →

Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, phylogenetics | Tagged , , , , | 1 Comment

Results of the Molecular Ecologist's Survey on High-Throughput Sequencing

Posted on 11 Apr, 2016 by Elin Videvall

Some days ago, we asked our readers to fill in a survey (now closed) on your use of high-throughput sequencing techniques. We got a lot of responses, a total of 260 people filled in the form. Thank you! Here are the results of your answers. The … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing | Tagged , , , , | 1 Comment

The dangers of not thinking about the relics

Posted on 31 Mar, 2016 by Kelle Freel

No, I’m not talking about Saint Erik’s skull from his beheading in 1160, which (as it turns out) might just be real. A hot topic in microbiology is a different kind of relic. Amazing developments in microbial ecology in recent years … Continue reading →

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

The Molecular Ecologist's Survey on High-Throughput Sequencing

Posted on 31 Mar, 2016 by Elin Videvall

Last week we updated the Field Guide to Next Generation DNA Sequencers to better reflect the sequencing techniques of 2016. The NGS Field Guide is one of the most popular resources on the Molecular Ecologist web site, but we don’t know much about how our readers use … Continue reading →

Posted in bioinformatics, genomics, methods, next generation sequencing | Tagged , , , , | 2 Comments

RADseq vs. UCEs, round 3

Posted on 18 Mar, 2016 by Ethan Linck

Though reduced-representation genome sequencing (or high-throughput, or nextgen, or massively parallel sequencing, or…) has become standard practice for molecular ecology labs over the past few years, the relative merits of different library preparation methods remains an active area of research. … Continue reading →

Posted in bioinformatics, evolution, genomics, methods, next generation sequencing, phylogenetics | Tagged , , , | 1 Comment

Battle of the Text Editors

Posted on 16 Mar, 2016 by Katie Everson

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

Veritas Genetics offers $999 (human) genome sequences

Posted on 3 Mar, 2016 by Jeremy Yoder

Veritas Genetics, a company co-founded by Harvard University geneticist George Church* announced today that it will sequence your genome for less than $1,000. One dollar less, specifically. Up to now, “personal genome” services like 23andMe have used methods that don’t … Continue reading →

Posted in association genetics, bioinformatics, genomics, medicine, next generation sequencing | Tagged , , | 3 Comments

Geographical Heat Maps in R

Posted on 3 Mar, 2016 by Arun Sethuraman

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 , | 2 Comments