phyclust (version 0.1-30)

seq.data: A Toy Dataset in Class seq.data

Description

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 "-".

Format

This data contains a list with a seq.data structure described in the ‘Details’ section.

Author

Wei-Chen Chen

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.

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

See Also

print.seq.data.

Examples

if (FALSE) {
library(phyclust, quiet = TRUE)

seq.data.toy
seq.data.gap

par(mfrow = c(1, 2))
plotdots(seq.data.toy$org)
plotdots(seq.data.gap$org)
}