Author Archives: Mark Christie

About Mark Christie

Mark Christie is an assistant professor in the Department of Biological Sciences and Department of Forestry & Natural Resources at Purdue University.

A comparison of bioinformatics programming languages

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

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:

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 | 15 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 | 4 Comments