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[ Source: clustalw-mpi  ]

Package: clustalw-mpi (0.15-1) [multiverse]

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Download Source Package clustalw-mpi:

Maintainer:

Please consider filing a bug or asking a question via Launchpad before contacting the maintainer directly.

Original Maintainers (usually from Debian):

  • Debian-Med Packaging Team (Mail Archive)
  • Steffen Moeller
  • Andreas Tille
  • Charles Plessy

It should generally not be necessary for users to contact the original maintainer.

External Resources:

Similar packages:

MPI-distributed global sequence alignment with ClustalW

ClustalW is a popular tool for multiple sequence alignment. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is an MPI implementation of ClustalW. Based on version 1.82 of the original ClustalW, both the pairwise and progressive alignments are parallelized with MPI, a popular message passing programming standard. The pairwise alignments can be easily parallelized since the many alignments are time independent on each other. However the progressive alignments are essentially not parallelizable because of the time dependencies between each alignment.

Here the recursive parallelism paradigm is applied to the linear space profile-profile alignment algorithm. This approach is more time efficient on computers with distributed memory architecture. Traditional approach that relies on precomputing the profile-profile score matrix has also been implemented. Results shown the latter is indeed more appropriate for shared memory multiprocessor computer.

ClustalX is suggested for its support for local realignments, seaview is a versatile editor of alignments.

The original ClustalW/ClustalX can be found at URL: http://www.clustal.org/download/pre-2/

Other Packages Related to clustalw-mpi

  • depends
  • recommends
  • suggests
  • enhances
  • dep: lam-runtime
    LAM runtime environment for executing parallel programs
  • dep: libc6 (>= 2.4)
    Embedded GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: liblam4
    Shared libraries used by LAM parallel programs
  • sug: clustalx
    Multiple alignment of nucleic acid and protein sequences (graphical interface)
  • sug: seaview
    Multiplatform interface for sequence alignment and phylogeny
  • enh: clustalw
    global multiple nucleotide or peptide sequence alignment

Download clustalw-mpi

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 156.1 kB356.0 kB [list of files]
i386 136.8 kB348.0 kB [list of files]