odmix

An object of formal class <code>MsaAAMultipleAlignment</code>, as provided by the <pkg>msa</pkg> package.

msa_object

A string indicating the type of distance metric to be computed. Either <code>'linear'</code> and <code>'affine'</code> is supported at the moment.

distance_metric

Number of groups to fit in the mixture model. If a numeric vector of size <code>n</code>, <code>n</code> models will be fitted and a list of BIC values
will be given to choose a single model.

groups

This function performs clustering of biological sequences via fitting a
Gaussian mixture model of the distances defined by the <code>odseq</code> algorithm

Performs outlier detection of sequences in a multiple
        sequence alignment using bootstrap of predefined distance
        metrics. Outlier sequences can make downstream analyses
        unreliable or make the alignments less accurate while they are
        being constructed. This package implements the OD-seq algorithm
        proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for
        aligned sequences and a variant using string kernels for
        unaligned sequences.

Jose Jimenez

odseq

Outlier detection in multiple sequence alignments

odmix function

Gaussian mixture modelling of distances in a multiple sequence alignment.

A numeric matrix of size n x groups where the probability of belonging to a group is provided for each sequence.

prob

The class assigned according to <code>prob</code>. Returns a numeric vector.

class

BIC values for the models proposed in <code>groups</code>

odmix: Gaussian mixture modelling of distances in a multiple sequence alignment.

Description

Usage

Arguments

Value

See Also

Examples