‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures
Abstract Background Phylogenetic trees are essential diagrams used in different sciences, such as evolutionary biology or taxonomy, and they depict the relationships between a given set of taxa sharing a common ancestor. So far, a multitude of tools have already been developed to infer phylogeny, an...
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2025-06-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06178-1 |
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| author | Cristina Galisteo Rafael R. de la Haba |
| author_facet | Cristina Galisteo Rafael R. de la Haba |
| author_sort | Cristina Galisteo |
| collection | DOAJ |
| description | Abstract Background Phylogenetic trees are essential diagrams used in different sciences, such as evolutionary biology or taxonomy, and they depict the relationships between a given set of taxa sharing a common ancestor. So far, a multitude of tools have already been developed to infer phylogeny, and even more to visualize the resulting trees. However, editing generated graphical plots to obtain ready-to-publish figures is still a major issue. Most available tools do not take into consideration important aspects in nomenclature, such as the use of italics for taxon names or the superscript T that must be displayed after the strain/specimen designation to denote the type strain/specimen, at least not automatically. A gap also exists to easily highlight tree branches conserved across different phylogenies containing the same taxa. The lack of available tools to achieve these tasks is challenging for scientists, since manual formatting of phylogenetic trees is very time-consuming. Results Here, we present a tool named ‘gitana’, running in Linux/Windows/Mac operating systems with R software installed. It creates ready-to-publish trees with formatting taxon nomenclature and editing options such as rerooting, clade highlighting or collapsing, among other features. Moreover, ‘gitana’ performs node comparisons among phylogenies comprising the same taxa to identify conserved branches. Conclusions ‘gitana’ is a user-friendly tool to output high-quality and ready-to-publish phylogenetic trees for users without R-coding skills. It combines dedicated functions of popular R packages for phylogeny and graphical visualization into an easy one-line-command. The users’ manual and source code are freely available at https://github.com/cristinagalisteo/gitana . |
| format | Article |
| id | doaj-art-afb9193af12c4a1dae3a2a5000d6c978 |
| institution | OA Journals |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-afb9193af12c4a1dae3a2a5000d6c9782025-08-20T02:05:39ZengBMCBMC Bioinformatics1471-21052025-06-012611710.1186/s12859-025-06178-1‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figuresCristina Galisteo0Rafael R. de la Haba1Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaDepartment of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaAbstract Background Phylogenetic trees are essential diagrams used in different sciences, such as evolutionary biology or taxonomy, and they depict the relationships between a given set of taxa sharing a common ancestor. So far, a multitude of tools have already been developed to infer phylogeny, and even more to visualize the resulting trees. However, editing generated graphical plots to obtain ready-to-publish figures is still a major issue. Most available tools do not take into consideration important aspects in nomenclature, such as the use of italics for taxon names or the superscript T that must be displayed after the strain/specimen designation to denote the type strain/specimen, at least not automatically. A gap also exists to easily highlight tree branches conserved across different phylogenies containing the same taxa. The lack of available tools to achieve these tasks is challenging for scientists, since manual formatting of phylogenetic trees is very time-consuming. Results Here, we present a tool named ‘gitana’, running in Linux/Windows/Mac operating systems with R software installed. It creates ready-to-publish trees with formatting taxon nomenclature and editing options such as rerooting, clade highlighting or collapsing, among other features. Moreover, ‘gitana’ performs node comparisons among phylogenies comprising the same taxa to identify conserved branches. Conclusions ‘gitana’ is a user-friendly tool to output high-quality and ready-to-publish phylogenetic trees for users without R-coding skills. It combines dedicated functions of popular R packages for phylogeny and graphical visualization into an easy one-line-command. The users’ manual and source code are freely available at https://github.com/cristinagalisteo/gitana .https://doi.org/10.1186/s12859-025-06178-1Phylogenetic treeReady-to-publish treeConserved nodesNomenclatureTree formattingTree edition |
| spellingShingle | Cristina Galisteo Rafael R. de la Haba ‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures BMC Bioinformatics Phylogenetic tree Ready-to-publish tree Conserved nodes Nomenclature Tree formatting Tree edition |
| title | ‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures |
| title_full | ‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures |
| title_fullStr | ‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures |
| title_full_unstemmed | ‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures |
| title_short | ‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures |
| title_sort | gitana phylogenetic imaging tool for adjusting nodes and other arrangements a tool for plotting phylogenetic trees into ready to publish figures |
| topic | Phylogenetic tree Ready-to-publish tree Conserved nodes Nomenclature Tree formatting Tree edition |
| url | https://doi.org/10.1186/s12859-025-06178-1 |
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