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CUDAlign download for Linux

Free download CUDAlign Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named CUDAlign whose latest release can be downloaded as masa-cudalign- It can be run online in the free hosting provider OnWorks for workstations.

Download and run online this app named CUDAlign with OnWorks for free.

Follow these instructions in order to run this app:

- 1. Downloaded this application in your PC.

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- 3. Upload this application in such filemanager.

- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.

- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 6. Download the application, install it and run it.




CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information:
[1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. IEEE Transactions on Parallel and Distributed Systems, vol. 99, PrePrints, 2012
[2] Edans Sandes, Alba Melo. Smith-Waterman Alignment of Huge Sequences with GPU in Linear Space. IPDPS 2011: 1199-1211
[3] Edans Sandes, Alba Melo. CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. PPOPP 2010: 137-146

The latest source code can be found in Github. See the MASA project at https://github.com/edanssandes/MASA-CUDAlign



User interface

Java Swing, Command-line

Programming Language




This is an application that can also be fetched from https://sourceforge.net/projects/cudalign/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.