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README.md
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README.md

Phylogenies are rapidly becoming larger due to the rising number of available genomes. Beyond broad patterns, large phylogenies often become uninterpretable as tip labels are so small or excluded altogether. As a result, large phylogenies can be difficult to use for other researchers especially for groups interested in the relationships among a subset of taxa. Here, we introduce treehouse, a user friendly shiny app that allows researchers to obtain subtrees from large-scale phylogenies. Treehouse is populated with a handful of large-scale phylogenies available through treehouseDB. Additionally, treehouse features an additional function, userTree, which allows a user to upload and parse their own phylogeny.

Our aim is to make phylogenies more accessible to all and facilitate researchers exploration in their own phylogenies.

treehouse has been published as an open access article! Publication link

Quick Start

1) Installing dependencies

Function of this app requires the shiny and phytools R packages. To install these packages, execute the typical R command within the R environment.

install.packages("shiny", dep=T)
install.packages("phytools", dep=T)

Treehouse has been tested using
• R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
• phytools_0.6-60
• maps_3.3.0
• ape_5.3
• shiny_1.2.0

2) Opening up the shiny app

After installing dependencies run the shiny app by executing the following command in R

shiny::runGitHub("treehouse", "JLSteenwyk")

3) Input list of taxa

To view the evolutionary relationships between a set of taxa, click the "Browse..." button and select a file that has a single column of taxa names. For example, the file should look like the following:

Aspergillus_flavus
Aspergillus_oryzae
Aspergillus_fumigatus
Penicillium_solitum
Penicillium_antarcticum

See example_taxa_Aspergillaceae.txt as an example file in the present github repo

4) Download the result

To download the pdf of the phylogeny or the newick tree file, click "Download Plot" or "Download Newick File", respectively.

Additional vignettes

• See treehouse_vignettes.pdf for two additional vignettes on treehouse usage
• Vignette 1: Obtain a subtree of plant pathogens in the genera Aspergillus and Penicillium.
• Vignette 2: Obtain a subtree that allows for qualitative comparison of branch lengths for a faster- and slower-evolving lineage of budding yeast, Hanseniaspora.

Current phylogenies available

Animal

Taxa represented Number of tips Reference
Birds 198 taxa Prum, et al. 2015
Birds 48 taxa Jarvis et al. 2014
Insects 144 taxa Misof et al. 2014
Mammals 37 taxa Song et al. 2016
Mammals 36 taxa Tarver, et al. 2016
Metazoans 36 taxa Borowiec, et al. 2015
Metazoans 70 taxa Whelan, et al. 2015
Vertebrates 58 taxa Chen, et al. 2015
Worms 100 taxa Struck, et al. 2015

Fungi

Taxa represented Number of tips Reference
Aspergillus and Penicillium 81 taxa Steenwyk, et al. 2019
Cryptococcus neoformans 387 strains Desjardins et al. 2017
Fungi 214 taxa James et al. 2006
Agaricomycetes 5,284 taxa Varga et al. 2019
Saccharomyces cerevisiae 1,011 strains Peter, et al. 2018
Saccharomycotina 86 taxa Shen, et al. 2016
Saccharomycotina 332 taxa Shen, et al. 2018

Plant

Taxa represented Number of tips Reference
Caryophyllales 95 taxa Yang, et al. 2015
Flowering plants 45 taxa Xi et al. 2014
Land plants 103 taxa Wickett et al. 2014

Tree of Life

Taxa represented Number of tips Reference
Tree of Life 3,083 taxa Hug, et al. 2016

Please remember that these phylogenies are hypotheses; while most branches are robustly supported, a few show substantial conflict and should be treated with caution.

Contributions and feedback

Others are welcome to contribute phylogenies to treehouse as well as provide user feedback. To provide a phylogeny or feedback, please contact me at jacob[dot]steenwyk[at]vanderbilt[dot]edu. Thank you!

treehouse is developed and maintained by Jacob Steenwyk

Citation

If you found treehouse useful in your research, please cite
Steenwyk JL, Rokas A. 2019. Treehouse: a user-friendly application to obtain subtrees from large phylogenies. BMC Res. Notes 12:541. Link

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