A set of utilities for querying
'HaploReg' <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>,
'RegulomeDB' <http://www.regulomedb.org>
web-based tools. The package connects to
'HaploReg', 'RegulomeDB' searches and downloads results, without
opening web pages, directly from R environment.
Results are stored in a data frame that can be directly used in various
kinds of downstream analyses.

A set of utilities for querying
'HaploReg' <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>,
'RegulomeDB' <https://www.regulomedb.org/regulome-search/>
web-based tools. The package connects to
'HaploReg', 'RegulomeDB' searches and downloads results, without
opening web pages, directly from R environment.
Results are stored in a data frame that can be directly used in various
kinds of downstream analyses.

Reconstruction of Haplotype-Blocks from Time Series Data
Susanne U. Franssen, Nicholas H. Barton, Christian Schloetterer
Reconstruction of founder haplotype blocks from time series data.
igraph, foreach, zoo, stringi, matrixStats, gplots, stats,
dbscan, methods

Tool for Clustering Genotypes in Haplotypes
Sebastian Simondi <sebastian.simondi@gmail.com> and Gaston Quero, with
contributions from Victoria Bonnecarrere and Lucia Gutierrez
Function to  identify  haplotypes
within QTL (Quantitative Trait Loci). One haplotype is a combination of SNP
(Single Nucleotide Polymorphisms) within the QTL. This function groups
together all individuals of a population with the same haplotype.
Each group contains individual with the same allele in each SNP,
whether or not missing data. Thus, haplotyper groups individuals,
that to be imputed, have a non-zero probability of having the same alleles
in the entire sequence of SNP's. Moreover, haplotyper calculates such
probability from relative frequencies.

Haplotype Inference and Statistical Analysis of Genetic
Variation
Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and inferring haplotypes from DNA sequences or user provided absolute character difference matrix.  This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony.