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      ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications


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          Color may be very useful to visualise complex data. As far as taxonomy is concerned, color may help observing various species’ characteristics in correlation with classification. However, choosing the number of subclasses to display is often a complex task: on the one hand, assigning a limited number of colors to taxa of interest hides the structure imbedded in the subtrees of the taxonomy; on the other hand, differentiating a high number of taxa by giving them specific colors, without considering the underlying taxonomy, may lead to unreadable results since relationships between displayed taxa would not be supported by the color code. In the present paper, an automatic color coding scheme is proposed to visualise the levels of taxonomic relationships displayed as overlay on any kind of data plot. To achieve this goal, a dimensionality reduction method allows displaying taxonomic “distances” onto a Euclidean two-dimensional space. The resulting map is projected onto a 2D color space (the Hue, Saturation, Brightness colorimetric space with brightness set to 1). Proximity in the taxonomic classification corresponds to proximity on the map and is therefore materialised by color proximity. As a result, each species is related to a color code showing its position in the taxonomic tree. The so called ColorPhylo displays taxonomic relationships intuitively and can be combined with any biological result. A Matlab version of ColorPhylo is available at http://sy.lespi.free.fr/ColorPhylo-homepage.html. Meanwhile, an ad-hoc distance in case of taxonomy with unknown edge lengths is proposed.

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          Construction of phylogenetic trees.

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            Self-Organizing Maps

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              Dinucleotide relative abundance extremes: a genomic signature.

              Early biochemical experiments established that the set of dinucleotide odds ratios or 'general design' is a remarkably stable property of the DNA of an organism, which is essentially the same in protein-coding DNA, bulk genomic DNA, and in different renaturation rate and density gradient fractions of genomic DNA in many organisms. Analysis of currently available genomic sequence data has extended these earlier results, showing that the general designs of disjoint samples of a genome are substantially more similar to each other than to those of sequences from other organisms and that closely related organisms have similar general designs. From this perspective, the set of dinucleotide odds ratio (relative abundance) values constitute a signature of each DNA genome, which can discriminate between sequences from different organisms. Dinucleotide-odds ratio values appear to reflect not only the chemistry of dinucleotide stacking energies and base-step conformational preferences, but also the species-specific properties of DNA modification, replication and repair mechanisms.

                Author and article information

                Evol Bioinform Online
                Evolutionary Bioinformatics Online
                Libertas Academica
                13 November 2011
                : 7
                : 257-270
                [1 ]UMR INSERM unité U722 and Université Denis Diderot, Paris 7, Faculté de médecine, site Xavier Bichat, 16 rue Henri Huchard, 75870 Paris cedex 18, France
                [2 ]Laboratoire LSIS (UMR CNRS 6168), Equipe I&M (ESIL) case 925, 163, avenue de Luminy, 13288 Marseille cedex 9, France
                Author notes
                Corresponding author email: sylvain.lespinats@ 123456gmail.com
                © the author(s), publisher and licensee Libertas Academica Ltd.

                This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.

                Original Research

                Bioinformatics & Computational biology
                taxonomy,hierarchical classification,dimensionality reduction,color code


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