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.

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

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Files

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

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All documentation is copyright its authors; we didn't write any of that.