Index
A
- admixture
- population structure, investigating / Investigating population structure with admixture, How to do it...
- reference / Investigating population structure with admixture
- download link / Getting ready
- Airflow
- reference / Introduction
- variant analysis pipeline, deploying / Deploying a variant analysis pipeline with Airflow, How to do it…
- alignment data
- working with / Working with alignment data, Getting ready, How to do it...
- AmiGO
- reference / See also
- Anaconda
- reference / Introduction
- required software, installing / Installing the required software with Anaconda, Getting ready, How to do it...
- Anaconda distribution
- download link / How to do it...
- analysis
- dataset, preparing for / Preparing the dataset for analysis, How to do it…
- annotations
- genes, extracting from reference / Extracting genes from a reference using annotations, How to do it...
- API
- used, for accessing Galaxy / Accessing Galaxy using the API, Getting ready, How to do it…
- Arlequin
- reference / There's more...
B
- Basic local alignment search tool (BLAST) / There's more...
- basic sequence analysis
- performing / Performing basic sequence analysis, How to do it...
- bcbio-nextgen
- reference / See also
- Binary Alignment Map (BAM) / Introduction
- Bio.PDB / Introducing Bio.PDB, How to do it...
- Bio.PopGen
- datasets, exploring / Exploring a dataset with Bio.PopGen, Getting ready, How to do it...
- Bioblend
- reference / Accessing Galaxy using the API
- Bioconda
- reference / Installing the required software with Anaconda
- Bioconductor
- reference / See also
- bioinformatics
- pipeline systems / Introduction
- bioinformatics data
- generic pipelines, using with / Using generic pipelines with bioinformatics data, How to do it…
- Biopython
- reference / See also, See also
- mmCIF files, parsing / Parsing mmCIF files using Biopython, How to do it...
- Biopython SeqIO page
- reference / See also
- Biostars
- Browser Extensible Data (BED) / Processing NGS data with HTSeq, See also
- Burrows-Wheeler Aligner (bwa)
- about / Getting ready, Working with alignment data, There's more...
- reference / See also
- bzip2
- reference / Getting ready
C
- chloroquine resistance transporter (CRT) / How to do it...
- chromosome arm 3L
- download link / Getting ready
- code
- optimizing, with Cython / Optimizing code with Cython and Numba, How to do it...
- optimizing, with Numba / Optimizing code with Cython and Numba, How to do it...
- Complete Genomics data
- reference / See also
- complex demographic scenarios
- Comprehensive R Archive Network (CRAN)
- reference / There's more...
- Copy Number Variation (CNV) / There's more…
- copy number variations (CNVs) / Analyzing data in VCF, Introduction
- Cython
- code, optimizing / Optimizing code with Cython and Numba, How to do it...
- Cytoscape
- reference / Plotting protein interactions with Cytoscape the hard way
- protein interactions, plotting / Getting ready, How to do it...
D
- DADA2 plugin
- reference / How to do it...
- Dask
- parallel computing, performing / Doing parallel computing with Dask, How to do it...
- data
- analyzing, in VCF / Analyzing data in VCF, How to do it...
- exploring, decision trees used / Using decision trees to explore the data, How to do it…
- exploring, with standard statistics / Exploring the data with standard statistics, How to do it…
- databases
- protein, finding in / Finding a protein in multiple databases, How to do it...
- dataset
- preparing, for analysis / How to do it…
- datasets
- managing, with PLINK / Managing datasets with PLINK, Getting ready, How to do it...
- exploring, with Bio.PopGen / Exploring a dataset with Bio.PopGen, Getting ready, How to do it...
- preparing, for phylogenetic analysis / Preparing a dataset for phylogenetic analysis, How to do it...
- preparing, for analysis / Preparing the dataset for analysis, How to do it…
- decision trees
- used, for exploring data / Using decision trees to explore the data, How to do it…
- Deoxyhypusine Synthase (DHPS) / Simulating selection
- Dihydrofolate Reductase (DHFR) / Simulating selection
- Directed Acyclic Graph (DAG) / How to do it…
- Docker
- reference / Introduction, See also
- required software, installing / Installing the required software with Docker, Getting ready, How to do it..., See also
E
- Ebolavirus
- reference / Getting ready
- Ensembl
- reference / There's more...
- gene ontology information, retrieving from / Retrieving gene ontology information from Ensembl, How to do it...
- Ensembl REST API
- orthologues, finding / Finding orthologues with the Ensembl REST API, How to do it...
- ETE
- reference / There's more...
- extensions, IPython
- reference / See also
F
- F-statistics
- computing / Computing F-statistics, How to do it...
- reference / See also
- FASTQ
- reference / See also
- fastStructure
- first-in, first-out (FIFO) / How to do it...
- fixation index (FST) / Introduction
- FlyBase
- reference / See also
- forward-time simulations / Introducing forward-time simulations, How to do it...
G
- 1,000 Genomes Project
- reference / See also
- Galaxy
- reference / Introduction, Introducing Galaxy servers
- about / Introducing Galaxy servers
- installing / How to do it…
- accessing, API used / Accessing Galaxy using the API, Getting ready, How to do it…
- Galaxy tool
- developing / Developing a Galaxy tool, Getting ready, How to do it…
- GBIF datasets
- georeferencing / Georeferencing GBIF datasets, How to do it...
- GBIF REST interface
- reference / There's more...
- GenBank
- gene ontologies
- reference / See also
- Gene Ontology (GO) / Introduction, How to do it...
- gene ontology information
- retrieving, from Ensembl / Retrieving gene ontology information from Ensembl, How to do it...
- Genepop
- reference / Introduction
- about / Introducing the Genepop format, How to do it...
- General Transfer Format (GTF) / Traversing genome annotations
- Generic Feature Format (GFF) / Traversing genome annotations
- generic pipelines
- using, with bioinformatics data / Using generic pipelines with bioinformatics data, How to do it…
- genes
- extracting, from reference / Getting ready, How to do it...
- genetic data
- aligning / Aligning genetic and genomic data, How to do it...
- genome-wide association studies (GWAS) / Introduction
- genome accessibility
- Genome Analysis Toolkit (GATK)
- about / Getting ready, How to do it...
- reference / See also
- genome annotations
- traversing / Traversing genome annotations, How to do it...
- genomes
- high-quality reference genomes / Working with high-quality reference genomes
- organism genomes / Getting ready
- low-quality genome references / Dealing with low-quality genome references
- genomes, National Center for Biotechnology Information (NCBI)
- reference / See also
- genomic data
- aligning / Aligning genetic and genomic data, How to do it...
- genomic features
- finding, from sequencing annotations / Finding genomic features from sequencing annotations, How to do it…
- geometric operations
- performing / Performing geometric operations, How to do it...
- Gephi
- reference / There's more...
- Germline
- shared chromosomal segments, inferring / Inferring shared chromosomal segments with Germline, Getting ready, How to do it...
- GFF spec
- reference / See also
- ggplot
- reference / There's more...
- Global Biodiversity Information Facility
- reference / Accessing the Global Biodiversity Information Facility via REST
- accessing, via REST / How to do it...
- graphs
- reference / There's more...
H
- HapMap
- reference / Getting ready
- hard filters
- reference / Getting ready
- HDF Compass
- reference / Getting ready
- Hierarchical Data Format (HDF5)
- high-quality reference genomes
- working with / Working with high-quality reference genomes, Getting ready, How to do it...
- HTSeq
- reference / Processing NGS data with HTSeq
- NGS data, processing / Processing NGS data with HTSeq, How to do it...
- htslib package
- reference / Getting ready
I
- insertions/deletions (INDELs) / Analyzing data in VCF
- IPython magics
- reference / See also
- island model
- population structure, simulating / Simulating population structure using island and stepping-stone models, How to do it...
- IUPAC ambiguity codes
- reference / See also
J
- Java Virtual Machine (JVM) / Getting ready
- Jupyter Notebooks
- R magic, performing / Performing R magic with Jupyter Notebook, How to do it...
K
- Kyoto Encyclopedia of Genes and Genomes (KEGG)
- reference / There's more...
L
- last-in, first-out (LIFO) / How to do it...
- linkage disequilibrium
- reference / See also
- linkage disequilibrium (LD) pruning / Managing datasets with PLINK
- low-quality genome references
- dealing with / Dealing with low-quality genome references, Getting ready, How to do it...
M
- MAFFT
- reference / Aligning genetic and genomic data
- Mendelian error information
- using, for quality control / Using Mendelian error information for quality control, How to do it…
- metagenomics
- performing, with QIIME 2 Python API / Doing metagenomics with the QIIME 2 Python API, Getting ready, How to do it...
- mmCIF files
- parsing, with Biopython / Parsing mmCIF files using Biopython, How to do it...
- mmCIF format
- reference / There's more...
- modern sequence formats
- working with / Working with modern sequence formats, Getting ready, How to do it...
- molecular distances
- computing, on PDB file / Computing molecular distances on a PDB file, How to do it...
- MUSCLE
- reference / Aligning genetic and genomic data
- MySQL tables, for Ensembl
- reference / See also
N
- National Center for Biotechnology Information (NCBI)
- about / Accessing GenBank and moving around NCBI databases, How to do it...
- reference / See also
- NCBI databases
- about / Accessing GenBank and moving around NCBI databases, There's more...
- data, fetching from / How to do it...
- reference / See also
- NetworkX
- next-generation sequencing (NGS) / Introduction, Introduction
- NGS data
- processing, with HTSeq / Processing NGS data with HTSeq, How to do it...
- Numba
- code, optimizing / Optimizing code with Cython and Numba, How to do it...
O
- OpenStreetMap
- reference / Georeferencing GBIF datasets, There's more...
- orthologues
- finding, with Ensembl REST API / Finding orthologues with the Ensembl REST API, How to do it...
P
- page to paired-end reads, Illumina
- reference / See also
- pandas
- reference / See also
- Panther
- reference / See also
- parallel computing
- performing, with Dask / Doing parallel computing with Dask, How to do it...
- parallel processing, HDF5
- reference / There's more...
- Parquet
- PDB file
- information, extracting from / 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...
- Phred quality score
- reference / How to do it..., See also
- phylogenetic analysis
- dataset, preparing for / Preparing a dataset for phylogenetic analysis, How to do it...
- phylogenetic data
- visualizing / Visualizing phylogenetic data, How to do it...
- phylogenetics
- about / Introduction
- reference / See also
- phylogenetic trees
- reconstructing / Reconstructing phylogenetic trees, How to do it...
- constructing / How to do it...
- PhyloXML
- reference / See also
- Picard
- reference / See also
- Pillow
- reference / Georeferencing GBIF datasets
- pipelines / Introduction
- pipeline systems, bioinformatics
- Galaxy / Introduction
- Script of Scripts (SoS) / Introduction
- Apache Airflow / Introduction
- Planemo
- reference / Developing a Galaxy tool
- PlasmoDB
- reference / See also
- PLINK
- reference / Introduction, See also
- datasets, managing / Managing datasets with PLINK, Getting ready, How to do it...
- population genetics / Introduction
- population structure
- investigating, with admixture / Investigating population structure with admixture, How to do it...
- simulating, stepping-stone model used / Simulating population structure using island and stepping-stone models, How to do it...
- simulating, island model used / Simulating population structure using island and stepping-stone models, How to do it...
- Principal Components Analysis
- performing / Performing Principal Components Analysis, Getting ready, How to do it...
- references / See also
- protein
- finding, in multiple databases / Finding a protein in multiple databases, How to do it...
- Protein Data Bank (PDB) / Introduction
- protein interactions
- plotting, with Cytoscape / Plotting protein interactions with Cytoscape the hard way, How to do it...
- proteomics / Introduction
- pygraphviz library
- reference / See also
- PyMOL
- animating with / Animating with PyMOL, How to do it...
- references / Getting ready, There's more...
- pysamstats library
- reference / See also
- Python Global Interpreter Lock (GIL)
- reference / There's more...
- Python Package Index (PyPI) / Getting ready
Q
- QIIME 2
- reference / Getting ready
- QIIME 2 Python API
- metagenomics, performing / Doing metagenomics with the QIIME 2 Python API, Getting ready, How to do it...
- quality control
- Mendelian error information, using for / Using Mendelian error information for quality control, How to do it…
- QuickGO
- reference / See also
R
- R
- reference / See also
- RAxML
- reference / Getting ready
- reference genomes of model organisms, Ensembl
- reference / See also
- RepeatMasker
- reference / See also
- resilient distributed datasets (RDDs) / There's more...
- REST
- Global Biodiversity Information Facility, accessing / How to do it...
- REST API
- reference / There's more...
- rkt
- reference / See also
- R magic
- performing, with Jupyter Notebooks / Performing R magic with Jupyter Notebook, How to do it...
- R packages, for statistical genetics
- reference / See also
- rpy2
- interfacing, with R / Interfacing with R via rpy2, How to do it...
S
- SAM/BAM format
- reference / See also
- Sample Read Depth (DP) / How to do it...
- scikit-allel
- reference / There's more...
- Script of Scripts (SoS)
- reference / Introduction
- selection
- simulating / Simulating selection, How to do it...
- SEQanswers
- reference / See also
- SeqIO
- reference / How to do it...
- sequence alignment map (SAM) format / Working with alignment data
- Sequence Read Archive (SRA) / There's more...
- sequences
- comparing / Comparing sequences, How to do it...
- sequencing statistics
- computing, Spark used / Computing sequencing statistics using Spark, Getting ready, How to do it...
- shared chromosomal segments
- inferring, with Germline / Inferring shared chromosomal segments with Germline, Getting ready, How to do it...
- simuPOP
- reference / There's more...
- simuPOP programming / Getting ready
- Single-Nucleotide Polymorphism (SNP) / Introduction
- single-nucleotide polymorphisms (SNPs) / There's more...
- Singularity
- reference / See also
- SNP data
- SnpEff
- reference / Getting ready
- Spark
- sequencing statistics, computing / Computing sequencing statistics using Spark, Getting ready, How to do it...
- standard statistics
- used, for exploring data / Exploring the data with standard statistics, How to do it…
- stepping-stone model
- population structure, simulating / Simulating population structure using island and stepping-stone models, How to do it...
T
- third-party magic extensions, IPython
- reference / See also
- Tile Map Services
- reference / Georeferencing GBIF datasets
- tiling coordinates
- reference / There's more...
- trees
- working with / Playing recursively with trees, How to do it...
- reference / There's more...
- trimAl
- reference / Getting ready
U
- UCSC Genome Bioinformatics
- reference / There's more...
- UCSC genome browser
- reference / See also
- UniProt
- reference / There's more...
V
- variant analysis pipeline
- deploying, with Airflow / Deploying a variant analysis pipeline with Airflow, How to do it…
- Variant Call Format (VCF) / Introduction
- VCF
- data, analyzing in / Analyzing data in VCF, How to do it...
- reference / There's more..., See also
- VectorBase
- reference / See also
- Vertebrate Genome Annotation (Vega) project / How to do it...
- voltage-gated sodium channel (VGSC) gene / Extracting genes from a reference using annotations
W
- well-known text
- reference / There's more...
- whole genome sequencing (WGS) / Introduction
X
- Xcode
- reference / Getting ready
Z
- Zarr
- reference / There's more...