AlignStat: Comparison of Alternative Multiple Sequence Alignments

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.

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

View on CRAN

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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