odseq-package {odseq} | R Documentation |
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.
The DESCRIPTION file:
Package: | odseq |
Type: | Package |
Title: | Outlier detection in multiple sequence alignments |
Version: | 1.18.0 |
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_12 |
git_last_commit: | 7922c00 |
git_last_commit_date: | 2020-10-27 |
Date/Publication: | 2020-10-27 |
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.
José Jiménez
Maintainer: José Jiménez <jose@jimenezluna.com>
[1] OD-seq: outlier detection in multiple sequence alignments. Peter Jehl, Fabian Sievers and Desmond G. Higgins. BMC Bioinformatics. 2015.
library(msa) data(seqs) al <- msa(seqs) odseq(al, distance_metric = "affine", B = 1000, threshold = 0.025)