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
- 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
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
- First-In First-Out (FIFO)
- about / How to do it...
- Flybase
- URL / See also
- forward-time simulations
- 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
- 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
- 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
- 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
- Map Services
- median
- in large dataset, approximating / Computing the median in a large dataset, How to do it..., There's more...
- minimum allele frequency (MAF)
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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