Category Archives: howto

Into the Field

Posted on 2 Apr, 2013 by kimgilbert

A great migration is soon upon us.  I’m not talking about wildebeest, caribou, bar-headed geese, sandhill cranes, or any other of these amazing migratory feats.

Posted in howto | Tagged | 6 Comments

Fear and loathing in academia – Getting the right kind of mentorship

Posted on 12 Feb, 2013 by Mark Christie

This week I’ve invited a friend and colleague, Hayley Lanier, to contribute a guest post to the Molecular Ecologist.  Hayley is a Postdoctoral Fellow at the University of Michigan, where she works with Lacey Knowles.  She has contributed an excellent … Continue reading →

Posted in career, howto | 3 Comments

Making Maps with R

Posted on 18 Sep, 2012 by kimgilbert

First off, thanks to Tim and Jeremy for the invitation to write a guest post here on using R to make maps! As a brief introduction, my name is Kim Gilbert, and I am a Ph.D. student at the University … Continue reading →

Posted in howto, R, software | Tagged , , | 122 Comments

Calculating allele frequencies in R……

Posted on 7 Mar, 2012 by Mark Christie

Here is a simple annotated script to quickly calculate, output, and graph allele frequencies in R.  Here I have  downloaded data (via dryad) from Lander et al. 2011 of a European Beech data set genotyped at 13 microsatellite markers.  I … Continue reading →

Posted in bioinformatics, howto, software | 9 Comments

MoleculaR analyses with R:

Posted on 24 Feb, 2012 by Mark Christie

R is a powerful data analysis environment that has a large number of useful features.  Chief among them are: (1) it is open source and freely distributed, meaning you can download and install it on any computer you have access … Continue reading →

Posted in howto, software | 5 Comments

A penny for your method: Rohland and Reich (2012)

Posted on 28 Jan, 2012 by Jeremy Yoder

This post, which discussed results published by Rohland and Reich (2012), has been removed at the request of Beckman Coulter legal counsel.

Posted in howto, methods, next generation sequencing | 4 Comments

A penny for your method: Nutator

Posted on 2 Dec, 2011 by Brant Faircloth

This one requires a little ingenuity on your part (and perhaps some craft, duct tape, construction, and/or welding skills). A nutator (AKA nutating mixer or rotating mixer) is a gently rocking/rotating platform useful for continuously and gently mixing samples. They … Continue reading →

Posted in howto, methods, next generation sequencing | Leave a comment

Easing the pain of titration

Posted on 21 Sep, 2011 by Brant Faircloth

Quickly following up on Nick’s post re: Illumina Library Prep, Travis Glenn pointed me towards a manuscript in Nature Protocols that proposes an alternative to the oft-grumbled-about process of titrating libraries for 454/Ion Torrent sequencing: Zongli Zheng et al. Titration-free … Continue reading →

Posted in bioinformatics, howto, methods, next generation sequencing | 3 Comments

A Tweak to Illumina Library Prep

Posted on 19 Sep, 2011 by Nicholas Crawford

For those readers who are making Illumina libraries for NGS, which I assume is many of you, I’d like to direct you to this new paper by Sheila Fisher’s group at the Broad Institute. In this paper Fisher describes the … Continue reading →

Posted in bioinformatics, howto, methods, next generation sequencing | 1 Comment

Field Guide to Next Generation Sequencers now available

Posted on 8 Jun, 2011 by Tim Vines

Travis Glenn recently published a paper in ME Resources giving pricing and usage info for a range of NGS sequencers. Since this area is moving very fast, we’ve also put the tables from his paper up on the blog, and … Continue reading →

Posted in bioinformatics, howto, methods, next generation sequencing | 2 Comments