find.consensus {phyclust}R Documentation

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)

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.

Details

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

Value

A vector containing the consensus sequence with length L will be returned.

Author(s)

Wei-Chen Chen wccsnow@gmail.com

References

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

See Also

plotdots.

Examples

## Not run: 
library(phyclust, quiet = TRUE)

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

## End(Not run)
[Package phyclust version 0.1-18 Index]