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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.

173.

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

174.

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

176.

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.

177.

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.

178.

An alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.

179.

connect to a console server

181.

connect multiple user to a serial console with logging

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.

184.

ConTeXt documentation that is not DFSG free