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168.

The output of ClustalÂ[nbsp]W can be edited manually but preferably with an alignment editor like SeaView or within its companion ClustalÂ[nbsp]X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM.

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For details and citation purposes see paper "ClustalÂ[nbsp]W and ClustalÂ[nbsp]X version 2.0", Larkin M., et al. Bioinformatics 2007 23(21):2947-2948

170.

MPI-distributed global sequence alignment with ClustalW

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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.

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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.

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

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

175.

Multiple alignment of nucleic acid and protein sequences (graphical interface)

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This package offers a GUI interface for the Clustal multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated to highlight conserved features in the alignment. For professional presentations, one should use the texshade LaTeX package or boxshade.

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The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.