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.

Version: 1.3.1
Depends: R (≥ 2.10)
Imports: Rcpp (≥ 0.11.6), seqinr, ggplot2, reshape2, tools, utils
LinkingTo: Rcpp
Suggests: testthat
Published: 2016-09-16
Author: Thomas Shafee, Ira Cooke
Maintainer: Thomas Shafee <thomas.shafee at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
SystemRequirements: C++11
Materials: README
CRAN checks: AlignStat results


Reference manual: AlignStat.pdf
Package source: AlignStat_1.3.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X El Capitan binaries: r-release: AlignStat_1.3.1.tgz
OS X Mavericks binaries: r-oldrel: AlignStat_1.3.1.tgz
Old sources: AlignStat archive


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