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.

Documentation

Manual: AlignStat.pdf
Vignette: None available.

Maintainer: Thomas Shafee <thomas.shafee at gmail.com>

Author(s): Thomas Shafee, Ira Cooke

Install package and any missing dependencies by running this line in your R console:

install.packages("AlignStat")

Depends R (>= 2.10)
Imports Rcpp(>=0.11.6), seqinr, ggplot2, reshape2, tools, utils
Suggests testthat
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Package AlignStat
Materials
URL https://github.com/TS404/AlignStat
Task Views
Version 1.3.1
Published 2016-09-16
License GPL (>= 2)
BugReports https://github.com/TS404/AlignStat/issues
SystemRequirements C++11
NeedsCompilation yes
Citation
CRAN checks AlignStat check results
Package source AlignStat_1.3.1.tar.gz