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Category Archives: software
Best Practices for Scientific Computing…And Molecular Ecology?
Source: http://xkcd.com/292 *Update* Best Practices in Computing has now been published in PLoS Biology! Computers and computational techniques have significantly advanced the molecular ecologist’s toolbox for answering interesting and complex questions about a range of biological systems, model or otherwise. Imagine, … Continue reading
Posted in bioinformatics, data archiving, population genetics, science publishing, software
Tagged Computing
1 Comment
Making Maps with R
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
Approximate Bayesian computation without the wait
Approximate Bayesian computation (abc) is arguably one of the most exciting, and quickly developing, tools available to modern population geneticists . Requiring a combination of large scale simulations and the evaluation of summaries of simulated datasets and an observed dataset, … Continue reading
Posted in bioinformatics, software
Tagged approximate Bayesian computation, Bayesian population genetics, methods
4 Comments
Calculating pair-wise, unbiased Fst with R:
Calculating Weir and Cockerham’s FST is very useful because it is unbiased with respect to sample size (Weir and Cockerham 1984). Without adjusting allele frequency estimates with respect to sample sizes, estimates of FST can be upwardly biased (see Waples … Continue reading
Posted in methods, population genetics, software
16 Comments
Calculating allele frequencies in R……
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:
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
Code rongorongo*
Open-sourcing computer programs used as part of a scientific research program is important to supporting the validity of the research conducted and enabling progress in many fields. Yet, the issue of making computer code widely available is not without complication. Continue reading
Posted in software
4 Comments
Surfing the Wave
As Dilara pointed out in her recent post, keeping track of all the new papers, programs, and techniques is an enormous challenge for the busy molecular ecologist. These days it seems that one should be following publications in Molecular Ecology, Molecular Ecology Resources (of course!), TrEE, Science, Nature, Ecology, PNAS, BMC Evolutionary Biology, and PLoS biology/genetics*. Of course, this doesn’t include those journals specific to your particular sub-discipline.
– Finding New Papers –
The simplist way to keep track of new papers is with Google Reader. Google Reader, if you’re unaware, is google’s online Really Simple Syndication (RSS) reader. Basically, it lets you follow RSS feeds from searches on Pubmed, journals themselves, or blogs. In then colates on all the feed entries onto a single webpage. Essentially, you a list of journals and sublists with the most recent publications, abstracts, and links to the full articles. It definitely beats getting monthly table of contents emails. Continue reading