Journal Article

‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures

de la Haba, Rafael R., Galisteo, Cristina

2025

Overview

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 .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Bioinformatics / Biomedical and Life Sciences / Computational biology / Computational Biology - methods / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer Graphics / Conserved nodes / Developmental biology / Editing / Encyclopedias / Evolutionary biology / Genomes / Imaging systems / Life Sciences / Microarrays / Microbial taxonomy / Names / Nomenclature / Nomenclatures / Operating systems / Phylogenetic tree / Phylogenetic trees / Phylogenetics / Phylogeny / Programming languages / Prokaryotes / Ready-to-publish tree / Software / Source code / Taxa / Taxonomy / Tree edition / Tree formatting / Trees / Zoology