odseq-package {odseq}R Documentation

Outlier detection in multiple sequence alignments

Description

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.

Details

The DESCRIPTION file:

Package: odseq
Type: Package
Title: Outlier detection in multiple sequence alignments
Version: 1.20.0
Date: 2015-12-20
Author: José Jiménez
Maintainer: José Jiménez <jose@jimenezluna.com>
Description: 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.
License: MIT + file LICENSE
LazyData: True
Encoding: UTF-8
biocViews: Alignment, MultipleSequenceAlignment
VignetteBuilder: knitr
Suggests: knitr(>= 1.11)
Depends: R (>= 3.2.3)
Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1)
NeedsCompilation: no
git_url: https://git.bioconductor.org/packages/odseq
git_branch: RELEASE_3_13
git_last_commit: a873deb
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19

Index of help topics:

odmix                   Gaussian mixture modelling of distances in a
                        multiple sequence alignment.
odseq                   Outlier detection in a multiple sequence
                        alignment
odseq-package           Outlier detection in multiple sequence
                        alignments
odseq_unaligned         Outlier detection provided a
                        distance/similarity matrix of sequences.
seqs                    PFAM plus random data.

Author(s)

José Jiménez

Maintainer: José Jiménez <jose@jimenezluna.com>

References

[1] OD-seq: outlier detection in multiple sequence alignments. Peter Jehl, Fabian Sievers and Desmond G. Higgins. BMC Bioinformatics. 2015.

See Also

odseq odseq_unaligned

Examples

library(msa)
data(seqs)
al <- msa(seqs)
odseq(al, distance_metric = "affine", B = 1000, threshold = 0.025)

[Package odseq version 1.20.0 Index]