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Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format.
LaNet-vi provides images of large scale networks on a two-dimensional layout. The algorithm is based on the k-core and k-dense (m-core) decomposition. For more details see http://lanet-vi.fi.uba.ar.
XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
...It makes the search more efficient by using different data like conservation and binding scores about relevant promoter areas.
It is implemented as a part of Barchelor thesis work of Timo Petmanson
available here: http://comserv.cs.ut.ee/forms/ati_report/downloader.php?file=0701eb033c3bad8d3be4a79a29c70107c1cad745
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Software package for biological sequence analysis and better organization of the sequence data.
Uses a modified version of alistat from Sean Eddy's group Squid package (http://selab.wustl.edu/cgi-bin/selab.pl?mode=software)