Gotoh (0.9)

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C++ Wrapper for R which Does Alignments using Gotoh Algorithm.

http://cran.r-project.org/web/packages/Gotoh

Implement a Gotoh approach to sequence alignment. The Gotoh algorithm was first published by Osamu Gotoh in 1982; for more information please refer to: 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.

Maintainer: Rafael Nozal Canyadas
Author(s): Rafael Nozal Canyadas <rca025@uib.no> , Eivind Valen <eivind.valen@gmail.com>

License: GPL (>= 2)

Uses: Rcpp

Released almost 4 years ago.


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