A toy dataset, seq.data.toy, with 100 nucleotide sequences
and 200 sites in 4 clusters.
seq.data.gap contains some missing values indicated by "-".
Arguments
Format
This data contains a list with a seq.data structure described
in the ‘Details’ section.
Details
A toy dataset is generated to demonstrate phyclust.
It has 100 nucleotide sequences and 200 sites in 4 clusters
where the ancestral tree height 0.15 and the descendant tree height 0.09,
and sequences are evolved by a HKY85 model.
The structre of class seq.data is a list containing:
code.type
either "NUCLEOTIDE" or "SNP".
info
header for phylip file.
nseq
number of sequences, \(N\).
seqlen
length of sequences, \(L\).
seqname
sequence names.
org.code
original codes, dim = \(N\times L\).
org
transfered ids, dim = \(N\times L\).
byrow
TRUE for dim = \(N\times L\), FALSE for transpose.