Title: Tool for Clustering Genotypes in Haplotypes
Author: Sebastian Simondi <sebastian.simondi@gmail.com> and Gaston Quero, with
Description: 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.
whether or not missing data. Thus, haplotyper groups individuals,
in the entire sequence of SNP's. Moreover, haplotyper calculates such

Title: Haplotype Inference and Statistical Analysis of Genetic
Description: 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.

Title: Manipulating DNA Sequences and Estimating Unambiguous Haplotype
Description: 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 collapses identical DNA sequences into haplotypes or inferring haplotypes using user provided absolute pairwise character difference matrix.  This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.
Imports: methods, stats, utils, network, sna, ape, phangorn,

Imports: methods, stats, utils, network, sna, ape, phangorn,plotrix

Description: 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 collapses identical DNA sequences into haplotypes or infering haplotypes using user provided absolute pairwise character difference matrix.  This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.
Imports: methods, stats, utils, network, sna, ape, phangorn, pegas,