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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

Product type Paperback

Published in Nov 2018

Publisher Packt

ISBN-13 9781789344691

Length 360 pages

Edition 2nd Edition

Languages

Python

Tools

Biopython

Concepts

Bioinformatics

Author (1):

Tiago Antao

View More author details

Table of Contents (12) Chapters

Preface

1. Python and the Surrounding Software Ecology

2. Next-Generation Sequencing FREE CHAPTER

3. Working with Genomes

4. Population Genetics

5. Population Genetics Simulation

6. Phylogenetics

7. Using the Protein Data Bank

8. Bioinformatics Pipelines

9. Python for Big Genomics Datasets

10. Other Topics in Bioinformatics

11. Advanced NGS Processing

Preparing a dataset for phylogenetic analysis

In this recipe, we will download and prepare the dataset to be used for our analysis. The dataset contains complete genomes of the Ebola virus. We will use DendroPy to download and prepare the data.

Getting ready

We will download complete genomes from GenBank; these genomes were collected from various Ebola outbreaks, including several from the 2014 outbreak. Note that there are several virus species that cause the Ebola virus disease; the species involved in the 2014 outbreak (the EBOV virus, formally known as the Zaire Ebola virus) is the most common, but this disease is caused by more species of the genus Ebolavirus; four others are also available in sequenced form. You can...

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Authors (1)

Tiago Antao

Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto (Portugal) and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.

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