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 gmail.com> |
| BugReports: | https://github.com/TS404/AlignStat/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/TS404/AlignStat |
| 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: AlignStat_1.3.1.zip, r-release: AlignStat_1.3.1.zip, r-oldrel: AlignStat_1.3.1.zip |
| 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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