AlignStat: Comparison of Alternative Multiple Sequence Alignments

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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.

Author
Thomas Shafee, Ira Cooke
Date of publication
2016-09-16 12:55:27
Maintainer
Thomas Shafee <thomas.shafee@gmail.com>
License
GPL (>= 2)
Version
1.3.1
URLs

View on CRAN

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

Files in this package

AlignStat
AlignStat/tests
AlignStat/tests/testthat.R
AlignStat/tests/testthat
AlignStat/tests/testthat/AlignmentB.clustal
AlignStat/tests/testthat/AlignmentA.fasta
AlignStat/tests/testthat/prepared_ref.rda
AlignStat/tests/testthat/GrammicidinsClustal.fasta
AlignStat/tests/testthat/results.rda
AlignStat/tests/testthat/prprepared_ref.rda
AlignStat/tests/testthat/categories.rda
AlignStat/tests/testthat/AlignmentB.fasta
AlignStat/tests/testthat/prepared_com.rda
AlignStat/tests/testthat/means.rda
AlignStat/tests/testthat/GrammicidinsMuscle.fasta
AlignStat/tests/testthat/test-align.R
AlignStat/src
AlignStat/src/rcpp_align.cpp
AlignStat/src/RcppExports.cpp
AlignStat/NAMESPACE
AlignStat/data
AlignStat/data/comparison_alignment.rda
AlignStat/data/reference_alignment.rda
AlignStat/R
AlignStat/R/compare_alignments.R
AlignStat/R/data.R
AlignStat/R/RcppExports.R
AlignStat/R/AlignStat.R
AlignStat/R/Plots.R
AlignStat/README.md
AlignStat/MD5
AlignStat/DESCRIPTION
AlignStat/man
AlignStat/man/plot_similarity_heatmap.Rd
AlignStat/man/plot_similarity_summary.Rd
AlignStat/man/plot_dissimilarity_matrix.Rd
AlignStat/man/plot_dissimilarity_summary.Rd
AlignStat/man/comparison_alignment.Rd
AlignStat/man/plot_SP_summary.Rd
AlignStat/man/compare_alignments.Rd
AlignStat/man/reference_alignment.Rd
AlignStat/man/AlignStat.Rd