Goodbye 2013!

Retrospective blog post time, again! 2013 was a fine year. I was lucky enough to go to Bolivia:

…and to the Everglades in Florida to see manatees and gators, and to Knoxville, Tennessee for the AAPA meetings and the Great Smokey Mountains. With a bunch of great collaborators, I coauthored a papers on RADseq in primates, protein-protein interactions, and the use of phylogenetics in primate behavior. In our lab, data collection kicked into (relatively) high gear by prepping and sequencing about a dozen “next-gen” libraries full of primates. Amazingly, they all worked!

A big change in 2013 for me outside of the lab was to restart learning Spanish using the site, italki and to begin to learn halting French using Duolingo. The Spanish certainly came in handy in Bolivia (and Florida) and I hope the French will be equally useful if I ever work in Francophone Africa.

This here blog is just over a year and a half old. A bunch of folks (almost 30,000) visited this site from all over the world this year which always makes me happy. C’mon, though, Greenland! You’re STILL a lot of grey in this map projection.

Happy 2014!

Cheap Lab Gear from

After the announcement of Amazon’s tentative plans to deliver items via quadcopters, our lab members joked that it was only a matter of time before you can order restriction enzymes on Amazon and have them in hand before your frozen DNA thaws. (Turns out they do offer a few enzymes.) Below are the fruits of a brief search, a few plasticware items and lab notebooks that you can get for less than the big scientific supply companies:

Concatenate VCF SNPs into a FASTA Alignment

A while back I published a script, vcf-tab-to-fasta, to make a FASTA alignment from VCF tab files (output from VCFtoolsvcf-to-tab utility). It just concatenates the SNPs, but it’s useful as a quick sanity check when working with massive SNP datasets since you can then easily bang out a neighbor joining tree or compute pairwise distances, etc. I thought I’d be the only one to use it, but I was happy to have it available in an open source repository regardless.

I was heartened to discover that people have actually been downloading and using it, with over 100 downloads not counting those that checked it out via SVN. A user was nice enough to point out a bug—the script won’t work on haploid SNPs, such as those found on the Y chromosome or in the mitochondrial genome. Whoop! I had only ever used it on autosomal DNA. The bug is now fixed and I’ve written up a quick tutorial for its use. Check it out here, and let me know if you ever find it handy!