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| haplotypes-package | Haplotype inference and statistical analysis of genetic variation |
| append | Combines two 'Dna' objects |
| append-method | Combines two 'Dna' objects |
| append-methods | Combines two 'Dna' objects |
| as.data.frame | Coerces a 'Dna' object to a data.frame |
| as.data.frame-method | Coerces a 'Dna' object to a data.frame |
| as.data.frame-methods | Coerces a 'Dna' object to a data.frame |
| as.dna | Coerces an object to a 'Dna' object |
| as.dna-method | Coerces an object to a 'Dna' object |
| as.dna-methods | Coerces an object to a 'Dna' object |
| as.list | Methods for function 'as.list' in the Package 'haplotypes' |
| as.list-method | Methods for function 'as.list' in the Package 'haplotypes' |
| as.list-methods | Methods for function 'as.list' in the Package 'haplotypes' |
| as.matrix | Methods for function 'as.matrix' in the Package 'haplotypes' |
| as.matrix-method | Methods for function 'as.matrix' in the Package 'haplotypes' |
| as.matrix-methods | Methods for function 'as.matrix' in the Package 'haplotypes' |
| as.numeric | Coerces a 'Dna' object to a numeric matrix |
| as.numeric-method | Coerces a 'Dna' object to a numeric matrix |
| as.numeric-methods | Coerces a 'Dna' object to a numeric matrix |
| distance | Calculates absolute pairwise character difference matrix using a 'Dna' object |
| distance-method | Calculates absolute pairwise character difference matrix using a 'Dna' object |
| distance-methods | Calculates absolute pairwise character difference matrix using a 'Dna' object |
| Dna | Class '"Dna"' in the Package 'haplotypes' |
| Dna-class | Class '"Dna"' in the Package 'haplotypes' |
| dna.obj | Example DNA sequence data |
| grouping | Groups haplotypes according to the grouping variable (populations, species, etc.) |
| grouping-method | Groups haplotypes according to the grouping variable (populations, species, etc.) |
| grouping-methods | Groups haplotypes according to the grouping variable (populations, species, etc.) |
| Haplotype | Class '"Haplotype"' in the Package 'haplotypes' |
| haplotype | Methods for function 'haplotype' in the package 'haplotypes' |
| Haplotype-class | Class '"Haplotype"' in the Package 'haplotypes' |
| haplotype-method | Methods for function 'haplotype' in the package 'haplotypes' |
| haplotype-methods | Methods for function 'haplotype' in the package 'haplotypes' |
| haplotypes | Haplotype inference and statistical analysis of genetic variation |
| hapreord | Reorders haplotypes according to the ordering factor |
| hapreord-method | Reorders haplotypes according to the ordering factor |
| hapreord-methods | Reorders haplotypes according to the ordering factor |
| indelcoder | Codes gaps |
| indelcoder-method | Codes gaps |
| indelcoder-methods | Codes gaps |
| length | Methods for function 'length' in the package 'haplotypes' |
| length-method | Methods for function 'length' in the package 'haplotypes' |
| length-methods | Methods for function 'length' in the package 'haplotypes' |
| names | Function to get or set names of a 'Dna' object |
| names-method | Function to get or set names of a 'Dna' object |
| names-methods | Function to get or set names of a 'Dna' object |
| names<--method | Function to get or set names of a 'Dna' object |
| names<--methods | Function to get or set names of a 'Dna' object |
| ncol | Returns the length of the longest DNA sequence |
| ncol-method | Returns the length of the longest DNA sequence |
| ncol-methods | Returns the length of the longest DNA sequence |
| nrow | Returns the number of DNA sequences |
| nrow-method | Returns the number of DNA sequences |
| nrow-methods | Returns the number of DNA sequences |
| pairnei | Provides the average number of pairwise Nei's (D) differences between populations |
| pairnei-method | Provides the average number of pairwise Nei's (D) differences between populations |
| pairnei-methods | Provides the average number of pairwise Nei's (D) differences between populations |
| Parsimnet | Class '"Parsimnet"' in the Package 'haplotypes' |
| parsimnet | Estimates gene genealogies using statistical parsimony |
| Parsimnet-class | Class '"Parsimnet"' in the Package 'haplotypes' |
| parsimnet-method | Estimates gene genealogies using statistical parsimony |
| parsimnet-methods | Estimates gene genealogies using statistical parsimony |
| plot-method | Methods for function 'plot' in the package 'haplotypes' |
| plot-methods | Methods for function 'plot' in the package 'haplotypes' |
| polymorp | Displays polymorphic sites (base substitutions and indels) between two sequences |
| polymorp-method | Displays polymorphic sites (base substitutions and indels) between two sequences |
| polymorp-methods | Displays polymorphic sites (base substitutions and indels) between two sequences |
| read.fas | Read sequences from a file in FASTA format |
| show-method | Methods for function 'show' in the package 'haplotypes' |
| show-methods | Methods for function 'show' in the package 'haplotypes' |
| subs | Displays base substitutions |
| subs-method | Displays base substitutions |
| subs-methods | Displays base substitutions |
| [-method | Extract or replace parts of an object of class 'Dna' |
| [-methods | Extract or replace parts of an object of class 'Dna' |
| [<--method | Extract or replace parts of an object of class 'Dna' |