find.consensus

nid/sid matrix with $N$ rows/sequences and $L$ columns/sites.

code.type

FALSE (default) for no missing in consensus sequence.

with.missing

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.

programming

Phylogenetic clustering (phyloclustering) is an
        evolutionary Continuous Time Markov Chain model-based approach
        to identify population structure from molecular data without
        assuming linkage equilibrium. It provides a convenient
        implementation of phyloclustering for DNA and SNP data, capable
        of clustering individuals into subpopulations and identifying
        molecular sequences representative of those subpopulations. It
        is designed in C for performance, interfaced with R for
        visualization, and incorporates other popular open source
        software, ms, seq-gen and Hap-Clustering for simulating data
        and additional analyses. See the phyclust website for more
        information, documentations and examples.

find.consensus: Find the consensus sequence

Description

Usage

Arguments

Value

Details

References

See Also

Examples