seqAlign-package: Sequence Alignment
In ygu427/seqAlign: sequence alignment

Description Details Author(s) References

Functions in this package implement multiple sequences alignment, such as ClustalW, ClustalOmega and Muschle, and also pairwise sequence alignbment, such as Needleman-Wuntch algorithm and Smith-waterman algorithm.

Package:	seqAlign
Type:	Package
Version:	1.0
Date:	2015-12-01
License:	GPL-3

To use this package, you need to update the R to at least version 3.1 and install the package "msa","Biostrings","seqinr","biomaRt","tcltk". The most important function is pairAlign and msaAlign, which are the common user interface to pairwise alignment and multiple alignment respectively.

Keywords and phrases: pairwise sequence alignment, multiple sequence alignment, Needleman-Wunsch algorithm, Smith-Waterman algorithm, Clustal W program, Clustal Omega program, MUSCLE program

Yu Gu

Maintainer: Yu Gu <yu_gu@urmc.rochester.edu>

Bodenhofer, Ulrich, Enrico Bonatesta, Christoph Horejs-Kainrath, and Sepp Hochreiter. "msa: an R package for multiple sequence alignment." Bioinformatics (2015): btv494.

Durbin, Richard, Sean R. Eddy, Anders Krogh, and Graeme Mitchison. Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge university press, 1998.

ygu427/seqAlign documentation built on May 4, 2019, 2:33 p.m.