Book Image

Bioinformatics with Python Cookbook - Second Edition

By : Tiago Antao
Book Image

Bioinformatics with Python Cookbook - Second Edition

By: Tiago Antao

Overview of this book

Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data.
Table of Contents (16 chapters)
Title Page
About Packt
Contributors
Preface
Index

Modeling complex demographic scenarios


Here, we will show you how simuPOP can be extremely flexible for demographic modeling. We will simulate an age-structured population with different fecundity per age for males and different maximum litter sizes for females. In the middle of the simulation, we will remove all older females. We will study the effective population size across the simulation. Furthermore, we will simulate multiallelic loci this time (for example, for the simulation of microsatellites).

The removal of a part of the population can model many things; for example, the management of a conserved population in a national park, or the usage of insecticides in vector populations, or modeling the illegal poaching of animals. The applications of this kind of modeling are plenty.

Getting ready

We will have three age groups. The first age group will not be able to reproduce (modeling infants). The two older age groups can. Males of age two have twice the chance of mating than males of...