Author Archives: Mark Christie

A comparison of bioinformatics programming languages

Posted on 20 Nov, 2012 by Mark Christie

The times are a-changin and most molecular ecologists and evolutionary biologists are no longer asking themselves, “Should I learn a programming language?”, but rather “Which programming language should I learn?”. There are a variety of programming languages that are used by … Continue reading →

Posted in bioinformatics, next generation sequencing, software | 10 Comments

Linux: the glue that binds your next-generation sequencing analyses

Posted on 16 Oct, 2012 by Mark Christie

Would you like to use same operating system as 92% of the top 500 super computers?  Do you dig Japanese bullet trains, NASA, or the financial awesomeness that is the New York Stock Exchange?  Do you hate having to shell … Continue reading →

Posted in bioinformatics, next generation sequencing, population genetics | 5 Comments

Calculating pair-wise, unbiased Fst with R:

Posted on 14 May, 2012 by Mark Christie

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……

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