add.miss

alltest

as.sequence

calcclust

clsfyindels

clustersG

contr

distance2

ext.nodes

fillendgaps

fillna

geodist.corr

haplo

has.cycle

indtest

multipolypoz

pairneidist

pairPhiSTdist

parsnet

pegas.amova

polys

recdistG

ren.dupli

steplimit

tryconnect

tryconnectG

validity

xhaps

initialize-methods

initialize,Dna-method

initialize,Haplotype-method

initialize,Parsimnet-method

internal

haplotypes-internal

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.

Caner Aktas

haplotypes

Manipulating DNA Sequences and Estimating Unambiguous Haplotype
Network with Statistical Parsimony

haplotypes-internal function

Internal function(s) — haplotypes-internal

Internal function(s)

haplotypes-internal: Internal function(s)

Description

Arguments