Treehouse: a user-friendly application to obtain subtrees from large phylogenies

BMC Research Notes (2019) 12:541 Steenwyk and Rokas BMC Res Notes https://doi.org/10.1186/s13104-019-4577-5 Open Access RESEARCH NOTE Treehouse: a user‑friendly application to obtain subtrees from large phylogenies Jacob L. Steenwyk and Antonis Rokas* Abstract Objective: Phylogenetic trees that contain hundreds to thousands of taxa are now routinely generated. Retrieving the relationships among a subset of taxa in these large phylogenies can be a challenging or time-consuming task. Addressing this challenge requires the development of tools that facilitate the easy retrieval of subtrees from any user-specified set of taxa in a given phylogeny. Results: We developed treehouse, an open source tool that enables the retrieval of any subtree from a given large phylogeny. With a three-step workflow, treehouse successfully allows a user to obtain a subtree from any phylogeny. Treehouse can help researchers to explore the relationships among any set of taxa from across the tree of life. Treehouse is implemented as a shiny application in the R programming language. Treehouse software and usage instructions are publicly available at https://github.com/JLSteenwyk/treehouse. Keywords: Phylogenomics, Phylogenetics, Big data, Tree, Tree pruning, Shiny, Graphical user interface Introduction Evolutionary biology relies on understanding the phylogenetic relationships among sets of genes, traits, and organisms under investigation. However, large phylogenies that contain hundreds of taxa are increasingly becoming inaccessible to researchers interested in the relationships of just a few representatives. For example, some phylogenies are so large that taxon information is often challenging or impossible to visualize and is often excluded [1–4]; similarly, the lengths of many internal branches are often very short and the constraints of displaying a large tree in a letter-sized page make the tracing of relationships among a subset of taxa challenging and unnecessarily time-consuming. These issues will increase in frequency as the numbers of taxa included in phylogenies of genes, metagenomes, genomes, etc. continues to rapidly rise. To address these issues, we introduce treehouse, a user-friendly application with minimal dependencies that facilitates the retrieval of subtrees from any *Correspondence: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA user-specified set of taxa in a given phylogeny. Our simple three-step workflow allows users to obtain subtrees from a curated and growing database of large-scale phylogenetic trees from across the tree of life. Additionally, users may obtain subtrees from their own phylogenies which, can facilitate data exploration and inter-disciplinary collaboration. For easy integration into pre-existing project workflows, subtrees obtained from treehouse can be easily be downloaded as a newick file or PDF file that retains branch length information. Treehouse enables beginner and expert evolutionary biologists alike to reap the benefits of large-scale phylogenetic projects and use them to test evolutionary-based hypotheses. Main text Materials and methods Data acquisition The treehouse contains a database of 20 representative large phylogenies from across the tree of life (Table 1). Description of the software Using treehouse requires the R packages phytools, version 0.6–60 [21], and shiny, version 1.2.0 (https ://shiny.rstudio.com/). Dependencies of phytools © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Steenwyk and Rokas BMC Res Notes (2019) 12:541 Page 2 of 4 Table 1 Curated phylogenies currently available in treehouse’s database Highest level of taxonomic organization Taxon or taxa represented Number of taxa References Animals Birds 198 taxa [5] Animals Birds 48 taxa [6] Animals Insects 144 taxa [7] Animals Mammals 37 taxa [8] Animals Mammals 36 taxa [9] Animals Metazoans 36 taxa [10] Animals Metazoans 70 taxa [11] Animals Vertebrates 58 taxa [12] Animals Worms 100 taxa [13] Fungi Aspergillus and Penicillium 81 taxa [14] Fungi Cryptococcus neoformans 387 strains [15] Fungi Fungi 214 taxa [16] Fungi Agaricomycetes 5284 taxa [2] Fungi Saccharomyces cerevisiae 1011 strains [1] Fungi Saccharomycotina 86 taxa [17] Fungi Saccharomycotina 332 taxa [4] Plant Caryophyllales 95 taxa [18] Plant Flowering plants 45 taxa [19] Plant Land plants 103 taxa [20] Tree of life Tree of life 3083 taxa [3] includes maps, version 3.3.0 (https://cran.r-proje ct.org/web/packages/maps/index.html), and ape, version 5.3 [22]. To present the phylogeny as depicted by the original authors, phylogenies from treehouse’s database are rooted. The taxa chosen to root the phylogeny on are inferred from figures presented in the original manuscript or, in the case of phylogenies presented without taxa names, personal communications with the authors. Phylogenies are rooted using phytools’s root() function. Using the list of taxa provided by the user, treehouse determines the list of taxa to remove from the phylogeny using the setdiff() function. The resulting list is then used to remove taxa in the phylogeny using phytools’s drop.tip() function. To write out the resulting phylogeny in a newick-formatted text file or display it in a scalable-vector-graphic-formatted pdf file, we use the write.tree() and plot.phylo() functions in Ape, respectively. To create a user-friendly and intuitive user-interface, we used shiny. Results A three‑step workflow to obtain subtrees Treehouse is designed to have a simple user-interface that guides a user through an intuitive three-step workflow (Fig. 1A) and user interface (Fig. 1B). 1. Tree selection A user can choose between five tabs—userTree, Animals, Fungi, Plants, and Tree of Life—located at the top of the user interface (Fig. 1Ba). When using phylogenies from the treehouse database, a user selects the desired phylogeny using a dropdown menu (Fig. 1Bi; left). In userTree, a user selects a phylogeny in newick format from their local computer (Fig. 1Bi; right). 2. Selection of Taxa A user next uploads a text file containing the single-column list of taxa that they want a subtree for (Fig. 1Bii). Here, each taxon name must be identical to a taxon name in the full phylogeny. 3. Subtree output By clicking the ‘Update’ button, the user launches treehouse subtree retrieval. The subtree is (...truncated)