load_fasta

Loads a fasta file into matrix format ready for
running the hierBAPS algorithm.

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

load_fasta function

<dl><dt>msa</dt>
<dd>Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered</dd>
<dt>keep.singletons</dt>
<dd>A logical indicating whether to consider singleton mutations in calculating the clusters</dd></dl>

Arguments

load_fasta — load_fasta

<dl>

<dt>msa</dt>
<dd>Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered</dd>


<dt>keep.singletons</dt>
<dd>A logical indicating whether to consider singleton mutations in calculating the clusters</dd>

</dl>

load_fasta: load_fasta

Description

Usage

Value

Arguments

Examples