odseq: Outlier detection in multiple sequence alignments

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.

Author
José Jiménez
Date of publication
None
Maintainer
José Jiménez <jose@jimenezluna.com>
License
MIT + file LICENSE
Version
1.2.0

View on Bioconductor

Man pages

odmix
Gaussian mixture modelling of distances in a multiple...
odseq
Outlier detection in a multiple sequence alignment
odseq-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("odseq")}
odseq_unaligned
Outlier detection provided a distance/similarity matrix of...
seqs
PFAM plus random data.

Files in this package

odseq/DESCRIPTION
odseq/LICENSE
odseq/NAMESPACE
odseq/R
odseq/R/odmix.R
odseq/R/odseq.R
odseq/R/odseq_unaligned.R
odseq/build
odseq/build/partial.rdb
odseq/build/vignette.rds
odseq/data
odseq/data/seqs.RData
odseq/inst
odseq/inst/doc
odseq/inst/doc/vignette.R
odseq/inst/doc/vignette.Rmd
odseq/inst/doc/vignette.pdf
odseq/man
odseq/man/odmix.Rd
odseq/man/odseq-package.Rd
odseq/man/odseq.Rd
odseq/man/odseq_unaligned.Rd
odseq/man/seqs.Rd
odseq/vignettes
odseq/vignettes/vignette.Rmd