Index

A

• admixture
  • URL / Investigating population structure with Admixture, Getting ready
  • population structure, investigating with / Getting ready, How to do it…, There's more...
• aligned sequences
  • comparing / Comparing sequences, How to do it...
• alignment data
  • working with / Working with alignment data, How to do it…, There's more…, See also
• AmiGO
  • URL / See also
• Anaconda
  • URL / Introduction, See also
  • used, for installing software / Installing the required software with Anaconda, Getting ready, How to do it…, See also
  • distribution, URL / How to do it…
• animation
  • with PyMol / Animating with PyMol, How to do it..., There's more...
• annotations
  • used, for extracting genes from reference / Extracting genes from a reference using annotations, How to do it…, There's more...
• Anopheles genomes
  • URL / Getting ready
• Arlequin
  • about / There's more…
  • URL / There's more…
• arXiv
  • URL / See also
• awkward variations
  • URL / There's more...

B

• BED format
  • URL / See also
• Bio.PDB
  • about / Introducing Bio.PDB
  • using / Getting ready, How to do it..., There's more...
• Bio.Phylo
  • about / How to do it...
• Bio.PopGen
  • used, for exploring dataset / Exploring a dataset with Bio.PopGen, How to do it…, There's more...
• Bioconductor
  • URL / How to do it…, There's more…, See also
• Biopython
  • URL / See also, See also, See also
  • SeqIO page, URL / See also, How to do it…
  • coalescent, simulating with / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, There's more..., See also
  • about / Introduction
  • used, for parsing mmCIF files / Parsing mmCIF files using Biopython, How to do it...
• Biopython tutorial
  • URL / See also
• biostars
  • URL / See also, See also
• boot2docker
  • URL / Getting ready
• BWA
  • URL / See also
• bzip2
  • URL / Getting ready

C

• CDSs
  • URL / See also
• centromeres
  • URL / How to do it...
• Cholroquine Resistance Transporter (CRT) / How to do it…
• coalescent
  • simulating, with Biopython / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
  • simulating, with fastsimcoal / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
• code
  • optimizing, Cython used / Optimizing code with Cython and Numba, How to do it..., There's more...
  • optimizing, Numba used / Optimizing code with Cython and Numba, How to do it..., There's more...
• Coding Sequence (CDS) / How to do it…
• comprehensions
  • reference link / There's more...
• Copy Number Variation (CNVs) / Introduction
• CRAN
  • URL / There's more…
• Cython
  • used, for optimizing code / Optimizing code with Cython and Numba, How to do it..., There's more...
• Cytoscape
  • used, for plotting protein interactions / Plotting protein interactions with Cytoscape the hard way, How to do it...
  • URL / Plotting protein interactions with Cytoscape the hard way

D

• dataset
  • exploring, with Bio.PopGen / Exploring a dataset with Bio.PopGen, How to do it…, There's more...
• datasets
  • managing, with PLINK / Managing datasets with PLINK, Getting ready, How to do it…, There's more...
• Datasets.ipynb
  • URL / Getting ready
• DAVID
  • URL / See also
• decorators
  • URL / How to do it...
• demographic
  • complex demographic scenarios, modeling / Modeling complex demographic scenarios, Getting ready, How to do it…
• DendroPy
  • about / Introduction
• Docker
  • URL / Introduction, Getting ready
  • used, for installing software / Installing the required software with Docker, How to do it…, See also

E

• Ebola dataset
  • preparing / Preparing the Ebola dataset, How to do it..., There's more...
  • references / See also
• Ebolavirus
  • about / Getting ready
  • reference link / Getting ready
• EIGENSOFT
  • URL / Getting ready
• Ensembl
  • URL / There's more…, See also, See also
  • gene ontology information, retrieving / Retrieving gene ontology information from Ensembl, How to do it..., There's more...
• Ensembl REST API
  • used, for finding orthologues / Finding orthologues with the Ensembl REST API, How to do it..., There's more...
  • URL / There's more...
• ETE
  • about / There's more...
  • URL / There's more...
• executor
  • URL / There's more...
• exons
  • URL / See also
• extensions
  • URL / See also
  • third-party magic extensions, URL / See also

F

• F-statistics
  • computing / Computing F-statistics, How to do it…
  • URL / See also
• FASTQ format
  • URL / See also
• fastsimcoal
  • coalescent, simulating with / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, There's more..., See also
  • URL / Getting ready, See also
• fastStructure
  • URL / Investigating population structure with Admixture
• First-In First-Out (FIFO)
  • about / How to do it...
• Flybase
  • URL / See also
• forward-time simulations
  • about / Introducing forward-time simulations, How to do it..., There's more...
• FST (Fixation index) / Introduction

G

• GATK
  • URL / See also
• GATK annotated file
  • URL / Getting ready
• GBIF
  • about / Introduction
  • URL / Accessing the Global Biodiversity Information Facility
  • accessing / Accessing the Global Biodiversity Information Facility, How to do it..., There's more...
  • REST API, URL / There's more...
  • datasets, geo-referencing / Geo-referencing GBIF datasets, How to do it..., There's more...
  • REST interface, URL / There's more...
• GenBank
  • accessing / Accessing GenBank and moving around NCBI databases, How to do it…, There's more…
• GeneAlEx
  • URL / See also
• gene ontology
  • information, retrieving from Ensembl / Retrieving gene ontology information from Ensembl, How to do it..., There's more...
  • URL / There's more..., See also
• Gene Ontology (GO)
  • about / How to do it...
• Genepop
  • URL / Introduction, Getting ready, Getting ready
• Genepop format
  • about / Introducing the Genepop format, How to do it…
  • URL / See also
• generators
  • about / Thinking with generators, How to do it...
  • expressions, URL / See also
• genes
  • extracting from reference, annotations used / Extracting genes from a reference using annotations, How to do it…, There's more..., See also
• genetic data
  • aligning / Aligning genetic and genomic data, Getting ready, How to do it...
• genome
  • accessibility / Studying genome accessibility and filtering SNP data, How to do it…, There's more…, See also
• genomes
  • 1000 genomes project, URL / Interfacing with R via rpy2, See also
  • high-quality reference genomes / Working with high-quality reference genomes, Getting ready, How to do it..., There's more...
  • reference genomes, URL / See also
  • URL / See also, There's more...
  • annotations, traversing / Traversing genome annotations, How to do it..., There's more...
  • browser, URL / There's more...
• genomic data
  • aligning / Aligning genetic and genomic data, Getting ready, How to do it...
• genomics
  • data results FAQ, URL / See also
• geometric operations
  • performing / Performing geometric operations, How to do it..., There's more...
• Gephi
  • URL / There's more...
• GFF spec
  • URL / See also
• gffutils
  • URL / There's more...
• ggplot
  • URL / There's more…
• Git
  • URL / Getting ready, Getting ready, Getting ready
• Global Interpreter Lock (GIL)
  • URL / There's more...
• graph drawing
  • reference link / There's more...
• graphviz
  • URL / See also, Getting ready
  • about / Getting ready
• grep tool
  • about / How to do it...
• GTF
  • URL / See also

H

• HapMap
  • URL / Getting ready
• hydrogen detection
  • reference link / There's more...

I

• Illumina
  • URL / See also
• IPython
  • used, for performing R magic / Performing R magic with IPython, How to do it…
  • used, for performing parallel computing / Performing parallel computing with IPython, How to do it...
  • parallel architecture, URL / Getting ready
  • parallel functionality, URL / There's more...
• IPython magics
  • URL / See also
• IPython Notebook
  • URL / See also
• itertools
  • URL / How to do it...
• IUPAC ambiguity codes
  • URL / See also

K

• KEGG
  • URL / There's more...

L

• lambda function
  • reference link / There's more...
• Last-In First-Out (LIFO)
  • about / How to do it...
• lazyness
  • programming with / Programming with laziness, How to do it..., There's more...
• Linkage Disequilibrium
  • URL / See also

M

• MAFFT
  • about / Aligning genetic and genomic data
  • URL / Aligning genetic and genomic data
• Map Services
  • URL / Geo-referencing GBIF datasets
• median
  • in large dataset, approximating / Computing the median in a large dataset, How to do it..., There's more...
• minimum allele frequency (MAF)
  • about / Setting the stage for high-performance computing
• mitochondrial matrix
  • URL / There's more...
• mmCIF files
  • parsing, Biopython used / Parsing mmCIF files using Biopython, How to do it...
• mmCIF format
  • URL / There's more...
• molecular-interaction databases
  • accessing, with PSIQUIC / Accessing molecular-interaction databases with PSIQUIC, How to do it...
• molecular distances
  • computing, on PDB file / Computing molecular distances on a PDB file, How to do it...
• multiple databases
  • protein, finding / Finding a protein in multiple databases, How to do it..., There's more...
• MUSCLE
  • URL / Aligning genetic and genomic data
  • about / Aligning genetic and genomic data
• MySQL tables
  • URL / See also

N

• NCBI
  • about / Accessing GenBank and moving around NCBI databases
  • URL / Getting ready
  • data, searching / How to do it…, There's more…
  • data, fetching / How to do it…, There's more…
  • databases, URL / See also
• NetworkX graph processing library
  • URL / Plotting protein interactions with Cytoscape the hard way
• NGS
  • URL / See also
  • about / Introduction
• notebook
  • URL / Getting ready
• Numba
  • used, for optimizing code / Optimizing code with Cython and Numba, How to do it..., There's more...
  • URL / There's more...

O

• OpenStreetMap
  • URL / Geo-referencing GBIF datasets, There's more...
• orthologues
  • finding, Emsembl REST API used / Finding orthologues with the Ensembl REST API, How to do it..., There's more...

P

• P. falciparum genome
  • URL / Getting ready
• Panther
  • URL / See also
• parallel computing
  • performing, with IPython / Performing parallel computing with IPython, How to do it..., There's more...
• PCA
  • about / Performing Principal Components Analysis, How to do it…
  • URL / See also
• PDB file
  • information, extracting / Extracting more information from a PDB file, How to do it...
  • molecular distances, computing / Computing molecular distances on a PDB file, How to do it...
• PDB file format
  • reference link / Getting ready
• PDB parser
  • implementing / Implementing a basic PDB parser, How to do it..., There's more...
• Phred quality score
  • URL / How to do it…, See also
• phylogenetics
  • about / Introduction
• phylogenetic trees
  • reconstructing / Reconstructing phylogenetic trees, Getting ready, How to do it..., There's more...
  • rooted trees / Playing recursively with trees
  • unrooted trees / Playing recursively with trees
  • visualizing / Visualizing phylogenetic data, How to do it..., There's more...
• Picard
  • URL / See also
• Pillow
  • URL / Geo-referencing GBIF datasets
• PlasmoDB
  • URL / See also
• PLINK
  • URL / Introduction, How to do it…, See also, How to do it…, Getting ready
  • datasets, managing with / Managing datasets with PLINK, Getting ready, How to do it…, There's more..., See also
• poor human concurrent executor
  • designing / Designing a poor human concurrent executor, How to do it..., There's more...
• population structure
  • investigating, with admixture / Investigating population structure with Admixture, How to do it…, There's more...
  • URL / Investigating population structure with Admixture
  • simulating, island model used / Simulating population structure using island and stepping-stone models, How to do it…
  • simulating, stepping-stone model used / Simulating population structure using island and stepping-stone models, How to do it…
• Project Jupyter / Getting ready
• protein
  • finding, in multiple databases / Finding a protein in multiple databases, How to do it..., There's more...
• Protein Data Bank
  • about / Introduction
• protein interactions
  • plotting, Cytoscape used / Plotting protein interactions with Cytoscape the hard way, How to do it..., There's more...
• proteomics
  • about / Introduction
• PSI-MI TAB 2.7 format
  • URL / How to do it...
• PSIQUIC
  • URL / Accessing molecular-interaction databases with PSIQUIC
  • used, for accessing molecular-interaction databases / Accessing molecular-interaction databases with PSIQUIC, How to do it...
• pygenomics
  • URL / Getting ready, Getting ready, Getting ready, How to do it…
• pygraphviz
  • URL / Getting ready
  • about / Getting ready
• PyMol
  • used, for animation / Animating with PyMol, How to do it..., There's more...
  • URL / Getting ready, There's more...
• PyProt
  • URL / There's more...
• Python distribution
  • URL / See also
• Python library
  • URL / There's more...
• Python software
  • list / Getting ready

R

• R
  • URL / How to do it…, See also, See also
  • interfacing with, rpy2 used / Interfacing with R via rpy2, How to do it…, There's more…
  • magic, performing with IPython / Performing R magic with IPython
• RAxML
  • about / Getting ready
  • URL / Getting ready
• recursive programming
  • with trees / Playing recursively with trees, How to do it...
• reference
  • genes extracting from, annotations used / Extracting genes from a reference using annotations, How to do it…, There's more..., See also
• references
  • low-quality reference genomes / Dealing with low-quality genome references, Getting ready, How to do it..., There's more...
• RepeatMasker
  • URL / See also
• rpy2
  • used, for interfacing with R / Interfacing with R via rpy2, How to do it…, There's more…
• rpy library documentation
  • URL / See also

S

• SAM/BAM format
  • URL / See also
• seaborn
  • URL / Getting ready
• selection
  • simulating / Simulating selection, How to do it…
• SEQanswers
  • URL / See also
• Sequence Alignment/Map (SAM) format
  • URL / Working with alignment data
• sequence analysis
  • performing / Performing basic sequence analysis, How to do it…, There's more…
• sequence formats
  • working with / Working with modern sequence formats, Getting ready, How to do it…, There's more…, See also
• simcoal
  • URL / See also
• simulation
  • forward-time simulations / Introducing forward-time simulations, How to do it..., There's more...
  • selection / Simulating selection, How to do it…, There's more...
  • population structure, island model used / Simulating population structure using island and stepping-stone models, How to do it…
  • population structure, stepping-stone model used / Simulating population structure using island and stepping-stone models, How to do it…
  • coalescent, with fastsimcoal / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
  • coalescent, with Biopython / Simulating the coalescent with Biopython and fastsimcoal, How to do it…, See also
• simuPOP
  • about / Getting ready
  • URL / There's more...
• Single-nucleotide Polymorphisms (SNPs) / There's more…
• smartpca
  • URL / See also
• SNP data
  • filtering / Studying genome accessibility and filtering SNP data, Getting ready, How to do it…
• SnpEff
  • URL / Getting ready
• stage
  • setting, for high-performance computing / Setting the stage for high-performance computing, How to do it...
• Structural Bioinformatics FAQ
  • URL / Getting ready

T

• tiling coordinates
  • URL / There's more...
• TP53 protein
  • reference link / Introducing Bio.PDB
• trees
  • recursive programming / Playing recursively with trees, How to do it...
  • reference link / There's more...
• TrimAl
  • about / Getting ready
  • URL / Getting ready

U

• UCSC Genome Bioinformatics
  • URL / There's more…
• UCSC genome browser
  • URL / See also
• UniProt's REST interface
  • URL / There's more...

V

• VCF
  • data, analyzing / Getting ready, How to do it…
  • URL / See also
• VectorBase
  • URL / See also
• virtualenv
  • URL / There's more…

W

• well-known text
  • URL / There's more...
• Whole Genome Sequencing (WGS) / Introduction

X

• Xcode
  • URL / Getting ready