Category Archives: bioinformatics

Genome-wide effects of artificial selection

Posted on 12 Feb, 2015 by Arun Sethuraman

Humans have been artificially selecting for favorable traits in crops, pets, and livestock over millennia. Years of theoretical predictions and experimental evolution studies have shown the detrimental effects of increased homozygosity, and the population-wide advantages of artificially maintaining heterozygosity. Two … Continue reading →

Posted in bioinformatics, evolution, genomics, methods, mutation, population genetics, theory | Leave a comment

Phonemes and Genomes

Posted on 5 Feb, 2015 by Arun Sethuraman

Human phonemes and genomes are thought to have evolved hand-in-glove out of Africa. Several recent studies have attempted to capture a picture of this global variation in languages and peoples, often supporting (and rejecting) a serial founder model (eg. see … Continue reading →

Posted in bioinformatics, evolution, genomics, phylogenetics, population genetics | Tagged , , , | 1 Comment

SpaceMix, and a brief history of Spatial Genetics

Posted on 15 Jan, 2015 by Arun Sethuraman

Incorporating spatial data to inform studies of the population demography of a species has a long history of interest. From inferring geographical clines in Principal Components Analyses (Menozzi et al. 1978), using location data as “informative priors” during model-based estimation … Continue reading →

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

Totally RAD

Posted on 12 Dec, 2014 by Stacy Krueger-Hadfield

Puritz et al. (2014) weigh the pros and cons of, the aptly titled, “RAD fad” in a comment recently published online in Molecular Ecology. They challenge: (1) the assertion that the original RAD protocol minimizes the impact of PCR artifacts … Continue reading →

Posted in bioinformatics, genomics, methods, next generation sequencing, Uncategorized | 4 Comments

Migration Circos plots in R

Posted on 11 Dec, 2014 by Arun Sethuraman

We’ve all seen them – colorful, and I daresay, pretty darn informative. Circos plots are fun visualizations of large data-sets. I’ve seen them used in two contexts in comparative genomics – to represent structural variants in homologous chromosome segments in … Continue reading →

Posted in bioinformatics, genomics, howto, R, software | Tagged , | 11 Comments

Using GitHub with R and RStudio

Posted on 12 Nov, 2013 by Mark Christie

A few weeks back, The Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading →

Posted in bioinformatics, howto, R, software | 29 Comments

Sequencer to the stars

Posted on 5 Nov, 2013 by Jeremy Yoder

The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post. No single person is responsible for the revolution in genetic data collection that has reshaped biology over just a handful of decades, but if you had … Continue reading →

Posted in bioinformatics, book review, genomics | Leave a comment

Want to share your code?

Posted on 27 Aug, 2013 by kimgilbert

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading →

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments

How to Backup and Store your Next-Generation Sequencing (NGS) data

Posted on 6 Aug, 2013 by Mark Christie

Congratulations!  You have recently received a file path to retrieve your hard-earned next-generation sequencing data.  You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your … Continue reading →

Posted in bioinformatics, data archiving, genomics, howto | 1 Comment

Q&A: Julian Catchen helps us dig into STACKS – Part II

Posted on 11 Apr, 2013 by Mark Christie

As promised, below is part II of our interview with Julian Catchen. These questions focus more on the specifics of using stacks (i.e., user-related questions). Please see the first post if you are interested a general overview. Even more information, … Continue reading →

Posted in bioinformatics, genomics, howto, interview, methods | Tagged | Leave a comment