phyclust (version 0.1-9)

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.missing contains some missing values indicated by "-".

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: ll{ 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: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

print.seq.data.

Examples

seq.data.toy
seq.data.missing

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