Conventions

In this book, you will find a number of text styles that distinguish between different kinds of information. Here are some examples of these styles and an explanation of their meaning.

Code words in text, filenames, file extensions, URLs, user input, are shown as follows: "If you are using notebooks, open the 00_Intro/Interfacing_R notebook.ipynb and just execute the wget command on top."

A block of code is set as follows:

from collections import OrderedDict
import simuPOP as sp
pop_size = 100
pops = sp.Population(pop_size, loci=[1] * num_loci)
num_loci = 10
init_ops['Freq'] = sp.InitGenotype(freq=[0.5, 0.5])

Any command-line input or output is written as follows:

conda create -n bioinformatics biopython=1.65 python=3.4

New terms and important words are shown in bold. Words that you see on the screen, for example, in menus or dialog boxes, appear in the text like this: "The top line is without migration, the middle line with 0.005 migration and the bottom line with 0.1."