Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
Combines two Dna objects
Coerces a Dna object to a data.frame
Coerces an object to a Dna object
Coerces an object to a DNAbin object
Methods for function as.list in the Package haplotypes
Methods for function as.matrix in the Package haplotypes
Coerces an object to a network object
Coerces an object to a networx object
Coerces a Dna object to a numeric matrix
Coerces an object to a phyDat object
Calculates base composition
Generates single bootstrap replicate
Calculates absolute pairwise character difference matrix using a Dna...
Class "Dna" in the Package haplotypes
Groups haplotypes according to the grouping variable (populations, spe...
Class "Haplotype" in the Package haplotypes
Methods for function haplotype in the package haplotypes
Internal function(s)
Manipulating DNA Sequences and Estimating Unambiguous Haplotype Networ...
Reorders haplotypes according to the ordering factor
Provides the list of homoplastic indels and substitutions
Display DNA Sequence
Codes gaps
Methods for function length in the package haplotypes
Function to get or set names of a Dna object or Parsimnet object
Returns the length of the longest DNA sequence
Returns the number of DNA sequences
Provides the average number of pairwise Nei's (D) differences between ...
Provides the pairwise PhiST between populations
Class "Parsimnet" in the Package haplotypes
Estimates gene genealogies using statistical parsimony
Add Legends to Plots
Plots pie charts on statistical parsimony network
Methods for function plot in the package haplotypes
Displays polymorphic sites (base substitutions and indels) between two...
Returns the minimum and maximum lengths of the DNA sequences
Read sequences from a file in FASTA format
Removing gaps from Dna object
Retrieve or set the row names
Methods for function show in the package haplotypes
Displays base substitutions
Convert sequence characters from upper to lower case or vice versa
Extract Unique Sequences
Extract or replace parts of an object of class Dna
Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel-coding method (only simple indel-coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapsing 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.