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Category Archives: software
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
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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
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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
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Riding the Elephant
I recently received my first batch of reads from a single paired-end lane run on an Illumina Hi-Seq instrument. This batch totaled about 20 billion basepairs of DNA sequence, and the associated data files a combined 55.4 gigs of text. … Continue reading
Posted in bioinformatics, next generation sequencing, software
Tagged Cluster Computing, Hadoop, MapReduce, NGS, Python
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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.
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Posted in software
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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 readingEssential programmatic tools
There are essentials, and there are essentials. Here are several bioinformatics software libraries that I use on a daily basis
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Posted in bioinformatics, software
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