Extended Newick: it is time for a standard representation of phylogenetic networks
<p>Abstract</p> <p>Background</p> <p>Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutiona...
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| Format: | Article |
| Language: | English |
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BMC
2008-12-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/532 |
| _version_ | 1831599987725697024 |
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| author | Valiente Gabriel Rosselló Francesc Cardona Gabriel |
| author_facet | Valiente Gabriel Rosselló Francesc Cardona Gabriel |
| author_sort | Valiente Gabriel |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network).</p> <p>Results</p> <p>The standard we advocate as extended Newick format describes a whole phylogenetic network with <it>k </it>hybrid nodes as a single Newick string with <it>k </it>repeated nodes, and this representation is unique once the phylogenetic network is drawn or the ordering among children nodes is fixed. The extended Newick format facilitates phylogenetic data sharing and exchange, and also allows for the practical use of phylogenetic networks in computer programs and scripts. This standard has been recently agreed upon by a number of computational biologists, is already supported by several phylogenetic tools, and avoids the different drawbacks of using an a priori unknown number of Newick strings without any additional mark-up to represent a phylogenetic network.</p> <p>Conclusion</p> <p>The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetic networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.</p> |
| first_indexed | 2024-12-18T14:33:39Z |
| format | Article |
| id | doaj.art-7745f545668e48f6bea464027750fe91 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T14:33:39Z |
| publishDate | 2008-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-7745f545668e48f6bea464027750fe912022-12-21T21:04:32ZengBMCBMC Bioinformatics1471-21052008-12-019153210.1186/1471-2105-9-532Extended Newick: it is time for a standard representation of phylogenetic networksValiente GabrielRosselló FrancescCardona Gabriel<p>Abstract</p> <p>Background</p> <p>Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network).</p> <p>Results</p> <p>The standard we advocate as extended Newick format describes a whole phylogenetic network with <it>k </it>hybrid nodes as a single Newick string with <it>k </it>repeated nodes, and this representation is unique once the phylogenetic network is drawn or the ordering among children nodes is fixed. The extended Newick format facilitates phylogenetic data sharing and exchange, and also allows for the practical use of phylogenetic networks in computer programs and scripts. This standard has been recently agreed upon by a number of computational biologists, is already supported by several phylogenetic tools, and avoids the different drawbacks of using an a priori unknown number of Newick strings without any additional mark-up to represent a phylogenetic network.</p> <p>Conclusion</p> <p>The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetic networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.</p>http://www.biomedcentral.com/1471-2105/9/532 |
| spellingShingle | Valiente Gabriel Rosselló Francesc Cardona Gabriel Extended Newick: it is time for a standard representation of phylogenetic networks BMC Bioinformatics |
| title | Extended Newick: it is time for a standard representation of phylogenetic networks |
| title_full | Extended Newick: it is time for a standard representation of phylogenetic networks |
| title_fullStr | Extended Newick: it is time for a standard representation of phylogenetic networks |
| title_full_unstemmed | Extended Newick: it is time for a standard representation of phylogenetic networks |
| title_short | Extended Newick: it is time for a standard representation of phylogenetic networks |
| title_sort | extended newick it is time for a standard representation of phylogenetic networks |
| url | http://www.biomedcentral.com/1471-2105/9/532 |
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