Man pages for haplotypes
Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
| append-methods | Combines two 'Dna' objects |
| as.data.frame-methods | Coerces a 'Dna' object to a data.frame |
| as.DNAbin-methods | Coerces an object to a 'DNAbin' object |
| as.dna-methods | Coerces an object to a 'Dna' object |
| as.list-methods | Methods for function 'as.list' in the Package 'haplotypes' |
| as.matrix-methods | Methods for function 'as.matrix' in the Package 'haplotypes' |
| as.network-methods | Coerces an object to a 'network' object |
| as.networx-methods | Coerces an object to a 'networx' object |
| as.numeric-methods | Coerces a 'Dna' object to a numeric matrix |
| as.phyDat-methods | Coerces an object to a 'phyDat' object |
| basecomp-methods | Calculates base composition |
| boot.dna-methods | Generates single bootstrap replicate |
| distance-methods | Calculates absolute pairwise character difference matrix... |
| Dna-class | Class '"Dna"' in the Package 'haplotypes' |
| dna.obj | Example DNA sequence data |
| grouping-methods | Groups haplotypes according to the grouping variable... |
| Haplotype-class | Class '"Haplotype"' in the Package 'haplotypes' |
| haplotype-methods | Methods for function 'haplotype' in the package 'haplotypes' |
| haplotypes-internal | Internal function(s) |
| haplotypes-package | Manipulating DNA Sequences and Estimating Unambiguous... |
| hapreord-methods | Reorders haplotypes according to the ordering factor |
| homopoly-methods | Provides the list of homoplastic indels and substitutions |
| image-methods | Display DNA Sequence |
| indelcoder-methods | Codes gaps |
| length-methods | Methods for function 'length' in the package 'haplotypes' |
| names-methods | Function to get or set names of a 'Dna' object or 'Parsimnet'... |
| ncol-methods | Returns the length of the longest DNA sequence |
| nrow-methods | Returns the number of DNA sequences |
| pairnei-methods | Provides the average number of pairwise Nei's (D) differences... |
| pairPhiST-methods | Provides the pairwise PhiST between populations |
| Parsimnet-class | Class '"Parsimnet"' in the Package 'haplotypes' |
| parsimnet-methods | Estimates gene genealogies using statistical parsimony |
| pielegend-methods | Add Legends to Plots |
| pieplot-methods | Plots pie charts on statistical parsimony network |
| plot-methods | Methods for function 'plot' in the package 'haplotypes' |
| polymorp-methods | Displays polymorphic sites (base substitutions and indels)... |
| range-methods | Returns the minimum and maximum lengths of the DNA sequences |
| read.fas | Read sequences from a file in FASTA format |
| remove.gaps-methods | Removing gaps from 'Dna' object |
| rownames-methods | Retrieve or set the row names |
| show-methods | Methods for function 'show' in the package 'haplotypes' |
| subs-methods | Displays base substitutions |
| tolower-methods | Convert sequence characters from upper to lower case or vice... |
| unique-methods | Extract Unique Sequences |
| z[-methods | Extract or replace parts of an object of class 'Dna' |
