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TreeSnatcher plus: capturing phylogenetic trees from images

BACKGROUND: Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research. RESULT...

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Detalles Bibliográficos
Autores principales: Laubach, Thomas, von Haeseler, Arndt, Lercher, Martin J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411374/
https://www.ncbi.nlm.nih.gov/pubmed/22624611
http://dx.doi.org/10.1186/1471-2105-13-110
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author Laubach, Thomas
von Haeseler, Arndt
Lercher, Martin J
author_facet Laubach, Thomas
von Haeseler, Arndt
Lercher, Martin J
author_sort Laubach, Thomas
collection PubMed
description BACKGROUND: Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research. RESULTS: TreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel images. It offers a range of image pre-processing methods and detects the topology of a depicted tree with adequate user assistance. The user supervises the recognition process, makes corrections to the image and to the topology and repeats steps if necessary. At the end TreeSnatcher Plus produces a Newick tree code optionally including branch lengths for rectangular and freeform trees. CONCLUSIONS: Although illustrations of phylogenies exist in a vast number of styles, TreeSnatcher Plus imposes no limitations on the images it can process with adequate user assistance. Given that a fully automated digitization of all figures of phylogenetic trees is desirable but currently unrealistic, TreeSnatcher Plus is the only program that reliably facilitates at least a semi-automatic conversion from such figures into a machine-readable format.
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spelling pubmed-34113742012-08-04 TreeSnatcher plus: capturing phylogenetic trees from images Laubach, Thomas von Haeseler, Arndt Lercher, Martin J BMC Bioinformatics Software BACKGROUND: Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research. RESULTS: TreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel images. It offers a range of image pre-processing methods and detects the topology of a depicted tree with adequate user assistance. The user supervises the recognition process, makes corrections to the image and to the topology and repeats steps if necessary. At the end TreeSnatcher Plus produces a Newick tree code optionally including branch lengths for rectangular and freeform trees. CONCLUSIONS: Although illustrations of phylogenies exist in a vast number of styles, TreeSnatcher Plus imposes no limitations on the images it can process with adequate user assistance. Given that a fully automated digitization of all figures of phylogenetic trees is desirable but currently unrealistic, TreeSnatcher Plus is the only program that reliably facilitates at least a semi-automatic conversion from such figures into a machine-readable format. BioMed Central 2012-05-24 /pmc/articles/PMC3411374/ /pubmed/22624611 http://dx.doi.org/10.1186/1471-2105-13-110 Text en Copyright ©2012 Laubach et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Laubach, Thomas
von Haeseler, Arndt
Lercher, Martin J
TreeSnatcher plus: capturing phylogenetic trees from images
title TreeSnatcher plus: capturing phylogenetic trees from images
title_full TreeSnatcher plus: capturing phylogenetic trees from images
title_fullStr TreeSnatcher plus: capturing phylogenetic trees from images
title_full_unstemmed TreeSnatcher plus: capturing phylogenetic trees from images
title_short TreeSnatcher plus: capturing phylogenetic trees from images
title_sort treesnatcher plus: capturing phylogenetic trees from images
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411374/
https://www.ncbi.nlm.nih.gov/pubmed/22624611
http://dx.doi.org/10.1186/1471-2105-13-110
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