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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology

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Product type Paperback
Published in Jun 2015
Publisher
ISBN-13 9781782175117
Length 306 pages
Edition 1st Edition
Languages
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
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Table of Contents (16) Chapters Close

Bioinformatics with Python Cookbook
Credits
About the Author
About the Reviewers
www.PacktPub.com
Preface
1. Python and the Surrounding Software Ecology FREE CHAPTER 2. Next-generation Sequencing 3. Working with Genomes 4. Population Genetics 5. Population Genetics Simulation 6. Phylogenetics 7. Using the Protein Data Bank 8. Other Topics in Bioinformatics 9. Python for Big Genomics Datasets Index

Investigating population structure with Admixture


A typical analysis in population genetics was the one popularized by the program Structure (http://pritchardlab.stanford.edu/structure.html), which is used to study the population structure. This type of software is used to infer how many populations exist (or how many ancestral populations generate the current population) and how to identify potential migrants and admixed individuals. As Structure was developed quite some years ago when much less markers were genotyped (at that time, mostly a handful of microsatellites) and faster versions were developed, including one from the same laboratory called fastStructure (http://rajanil.github.io/fastStructure/). Here, we will use Python to interface with a program of the same type developed at UCLA called Admixture (https://www.genetics.ucla.edu/software/admixture/).

Getting ready

You will need to run the first recipe in order to use the hapmap10_auto_noofs_ld binary PLINK file. Again, we will use...

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