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167.
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This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. ClustalÂ[nbsp]W is very well accepted.
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Description
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(no translation yet)
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Located in
Package: clustalw
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168.
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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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Description
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(no translation yet)
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Located in
Package: clustalw
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169.
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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
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Description
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(no translation yet)
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Located in
Package: clustalw
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170.
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MPI-distributed global sequence alignment with ClustalW
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Summary
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Located in
Package: clustalw-mpi
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171.
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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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Description
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Located in
Package: clustalw-mpi
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172.
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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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Description
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(no translation yet)
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Located in
Package: clustalw-mpi
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173.
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ClustalX is suggested for its support for local realignments, seaview is a versatile editor of alignments.
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Description
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(no translation yet)
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Located in
Package: clustalw-mpi
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174.
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The original ClustalW/ClustalX can be found at URL: http://www.clustal.org/download/pre-2/
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Description
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Исходный ClustalW/ClustalX можно найти по ссылке: http://www.clustal.org/download/pre-2/
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Translated and reviewed by
Dmitry Tumaikin
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Located in
Package: clustalw-mpi
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175.
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Multiple alignment of nucleic acid and protein sequences (graphical interface)
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Summary
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Множественное выравнивание нуклеиновых кислот и белковых последовательностей (графический интерфейс)
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Translated by
Anton Patsev
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Reviewed by
CSRedRat
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Located in
Package: clustalx
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176.
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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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Description
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Этот пакет предоставляет графический интерфейс для Clustal - несколько программ выравнивания последовательности. Он предоставляет интегрированную среду для выполнения нескольких последовательностей и профиля выравнивания для анализа результатов. Последовательность выравнивания отображается в окне на экране. Универсальная цветовая схема была включена, чтобы выделить консервативные черты в выравнивании. Для профессиональных презентаций, следует использовать пакет texshade LaTeX или boxshade.
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Translated by
Anton Patsev
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Reviewed by
CSRedRat
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Located in
Package: clustalx
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