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Subsections

Perl Process management

Perl is frequently used to write custom analysis pipelines, which drives other programs and makes automated analyses.

Here we will look at how to write perl scripts which interact with other programs.

system()

Capturing output of external programs

Example of driving ms

Summary statistics

Biological problem

Let's say we have sequence data from two populations (e.g. Alaska mainland and Kodiak Island).

We are wondering whether the migration is one directional.

We want to run coalescent simulations under two different models, and look at the results of simulation to see whether the observed sequence data fits one of the model better.

Exercise: modify msDrive.pl

Instead of setting the migration rate to a pre-fixed value, modify the program to estimate the migration rate (in addition to divergence time). In other words, you need to draw the migration from a random distribution.


next up previous
Next: Approximate Bayesian Computation Up: coalsim Previous: Coalescent
Naoki Takebayashi 2011-11-09