phyclust (version 0.1-34)

find.consensus: Find the Consensus Sequence

Description

Based on the input data, this function will search all data along all sites to find a consensus sequence which may be or may not be one of the data.

Usage

find.consensus(X, code.type = .code.type[1], with.gap = FALSE)

Value

A vector containing the consensus sequence with length \(L\)

will be returned.

Arguments

X

nid/sid matrix with \(N\) rows/sequences and \(L\) columns/sites.

code.type

either "NUCLEOTIDE" (default) or "SNP".

with.gap

FALSE (default) for no gap in consensus sequence.

Author

Wei-Chen Chen

Details

X should be a numerical matrix containing sequence data that can be transfered by code2nid or code2sid.

References

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

See Also

plotdots.

Examples

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

find.consensus(seq.data.toy$org)
}