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This tool is interfaced with the statistical analysis software R (http://www.r-project.org/) which integrates a set of clustering programs that we detailed in Section 2.1.
As shown above, the combination of clustering programs gave better results than any single program.
Our work presents more general quantitative metrics that can be used as a standard for clustering programs.
Thus, the clustering programs combined in the TEdenovo pipeline do not generate systematic bias towards "incomplete" TEs of a given kind.
Although clustering programs for gene family classification can perform reasonably well in generating gene families, they need to be parameterized for optimal performance.
The algorithms for various clustering programs differed in their approach of clustering and combined use of such clustering tools with different algorithms fetched better results [ 97].
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CD-HIT clustering program was used to remove sequence redundancy by applying a global identity threshold of 90% and retaining the longest possible contigs.
We are currently working on combining BioProspector with a clustering program to explore gene expression networks and regulatory mechanisms.
Most of the files that are output by the clustering program are readable by TreeView (.cdt,.gtr,.atr), which allows you to browse clusters.
The clustering program begins with an initialization step where k initially clusters centers, called C k.
Section 3 proposes the objective and constraint conditions of the joint resource allocation and clustering programming.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com