AlignStat: Comparison of Alternative Multiple Sequence Alignments
Version 1.3.1

Methods for comparing two alternative multiple sequence alignments (MSAs) to determine whether they align homologous residues in the same columns as one another. It then classifies similarities and differences into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative to the other. Summarising these categories for each MSA column yields information on which sequence regions are agreed upon my both MSAs, and which differ. Several plotting functions enable easily visualisation of the comparison data for analysis.

Browse man pages Browse package API and functions Browse package files

AuthorThomas Shafee, Ira Cooke
Date of publication2016-09-16 12:55:27
MaintainerThomas Shafee <thomas.shafee@gmail.com>
LicenseGPL (>= 2)
Version1.3.1
URL https://github.com/TS404/AlignStat
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("AlignStat")

Man pages

AlignStat: AlignStat: A tool for the statistical comparison of...
compare_alignments: Compare alternative multiple sequence alignments
comparison_alignment: Comparison Alignment
plot_dissimilarity_matrix: A heatmap plot of the dissimilarity matrix of two multiple...
plot_dissimilarity_summary: An area plot summary of the different causes of column...
plot_similarity_heatmap: A heatmap plot of the column identities between two multiple...
plot_similarity_summary: A line plot summary of column similarity between two multiple...
plot_SP_summary: A line plot summary of sum of pairs score between two...
reference_alignment: Reference Alignment

Functions

AlignStat Man page
AlignStat-package Man page
PS Source code
SP Source code
SPprep Source code
compare_alignments Man page Source code
comparison_alignment Man page
degap_alignment Source code
import_alignment Source code
list_pairs Source code
percent Source code
plot_SP_summary Man page Source code
plot_dissimilarity_matrix Man page Source code
plot_dissimilarity_summary Man page Source code
plot_similarity_heatmap Man page Source code
plot_similarity_summary Man page Source code
prepare_alignment_matrix Source code
rcpp_align Source code
rcpp_prepare_alignment_matrix Source code
reference_alignment Man page
valid_alignments Source code

Files

tests
tests/testthat.R
tests/testthat
tests/testthat/AlignmentB.clustal
tests/testthat/AlignmentA.fasta
tests/testthat/prepared_ref.rda
tests/testthat/GrammicidinsClustal.fasta
tests/testthat/results.rda
tests/testthat/prprepared_ref.rda
tests/testthat/categories.rda
tests/testthat/AlignmentB.fasta
tests/testthat/prepared_com.rda
tests/testthat/means.rda
tests/testthat/GrammicidinsMuscle.fasta
tests/testthat/test-align.R
src
src/rcpp_align.cpp
src/RcppExports.cpp
NAMESPACE
data
data/comparison_alignment.rda
data/reference_alignment.rda
R
R/compare_alignments.R
R/data.R
R/RcppExports.R
R/AlignStat.R
R/Plots.R
README.md
MD5
DESCRIPTION
man
man/plot_similarity_heatmap.Rd
man/plot_similarity_summary.Rd
man/plot_dissimilarity_matrix.Rd
man/plot_dissimilarity_summary.Rd
man/comparison_alignment.Rd
man/plot_SP_summary.Rd
man/compare_alignments.Rd
man/reference_alignment.Rd
man/AlignStat.Rd
AlignStat documentation built on May 20, 2017, 3:13 a.m.