preproc_alignment

Preprocessed the snp matrix for hierBAPS.

Implements the hierarchical Bayesian analysis of populations structure (hierBAPS)
algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences
from multiple sequence alignments in FASTA format.
The implementation includes improved defaults and plotting capabilities
and unlike the original 'MATLAB' version removes singleton SNPs by default.

Gerry Tonkin-Hill

rhierbaps

Clustering Genetic Sequence Data Using the HierBAPS Algorithm

preproc_alignment function

<dl><dt>snp.matrix</dt>
<dd>A matrix containing SNP data. Rows indicate isolates and columns loci.</dd></dl>

Arguments

preproc_alignment — preproc_alignment

<dl>

<dt>snp.matrix</dt>
<dd>A matrix containing SNP data. Rows indicate isolates and columns loci.</dd>

</dl>

preproc_alignment: preproc_alignment

Description

Usage

Value

Arguments