Package: Gotoh
Type: Package
Title: C++ Wrapper for R which Does Alignments using Gotoh Algorithm
Version: 0.9
Date: 2015-05-18
Author: Rafael Nozal Canyadas <rca025@uib.no> , Eivind Valen <eivind.valen@gmail.com>
Maintainer: Rafael Nozal Canyadas <rca025@uib.no>
Description: Implement a Gotoh approach to sequence alignment. The Gotoh
             algorithm was first published by Osamu Gotoh in 1982; for more
             information please refer to: <doi:10.1016/0022-2836(82)90398-9>
             We are using 'Rcpp', which decrease greatly the CPU time with
             respect other alignment implementations. This was done in an
             effort to speed up the calculations for the project AmpliCan. The
             improvement we got compared with 'DECIPHER' is in between 300x and
             500x many fold for sequences between 100 to 200 nucleotides, and
             between 100x and 200x for sequences of between 200 to 300
             nucleotides. And up to 1.5x for sequences of size 10.000
             nucleotides and beyond. This package contains the minimum files
             require for it to work. Please download the repository at:
             https://rafanozal@bitbucket.org/rafanozal/amplican.git
             to get the a more verbose documentation and script benchmarks.
Depends: R (>= 3.1.1)
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp
Packaged: 2015-05-22 19:21:41 UTC; rafaelc
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-22 22:39:20
