Package Descriptions for Ubuntu

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167.
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.
 
Description
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Located in Package: clustalw
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.
 
Description
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Located in Package: clustalw
169.
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
 
Description
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Located in Package: clustalw
170.
MPI-distributed global sequence alignment with ClustalW
 
Summary
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Located in Package: clustalw-mpi
171.
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.
 
Description
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Located in Package: clustalw-mpi
172.
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.
 
Description
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Located in Package: clustalw-mpi
173.
ClustalX is suggested for its support for local realignments, seaview is a versatile editor of alignments.
 
Description
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Located in Package: clustalw-mpi
181.
connect multiple user to a serial console with logging
 
Summary
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Located in Package: conserver-server
182.
Conserver is an application that allows multiple users to watch a serial console at the same time. It can log the data, allows users to take write-access of a console (one at a time), and has a variety of bells and whistles to accentuate that basic functionality. The idea is that conserver will log all your serial traffic so you can go back and review why something crashed, look at changes (if done on the console), or tie the console logs into a monitoring system (just watch the logfiles it creates). With multi-user capabilities you can work on equipment with others, mentor, train, etc. It also does all that client-server stuff so that, assuming you have a network connection, you can interact with any of the equipment from home or wherever.
 
Description
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Located in Package: conserver-server Package: conserver-client
185.
The web site of ConTeXt provides a plethora of documents in pdf format documenting many features of ConTeXt and friends. These documents are only available as pdf documents.
 
Description
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Located in Package: context-doc-nonfree
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Contributors to this translation: Aleksey Kabanov, Alexander Ilyashov, Alexander Vasilyev, Alexey Androsov, Andrey Olykainen, Anton Patsev, Artem, CraZy_DeveLopeR, Dmitry Ledyaev, Dmitry Tumaikin, Eugene Roskin, Evgeny, Intervision, MadGreM, Maxim Kochetkov aka fido_max, Maxim Petrov, Michael Vogt, Minakov Arthur, Oleg Koptev, Oleg Yermakov, Pavel, Petr E. Antonov, Sergey "Shnatsel" Davidoff, Sergey Basalaev, Sergey Sedov, brutal_atom, ehpc, mikhail2704, qxov, trumen, vasilisc, vofka, vollossy, Даниил Рыжков.