TaxOnTree: Including taxonomic information in phylogenetic trees

Sakamoto T. and J. M. Ortega

TaxOnTree is a bioinformatics tool that embeds taxonomic information from NCBI Taxonomy into phylogenetic trees. TaxOnTree generates trees that allow users to easily access the taxonomic information of all entities comprising the tree.

Prerequisites

• Unix Platform;

  TaxOnTree was tested on Ubuntu, CentOS and MacOS, but it should work on any Unix platforms.

• Perl;

  Almost all Unix platforms have Perl 5 installed. To verify that, type perl -v in a command shell. If not, follow the instructions on [Perl website] (https://www.perl.org/get.html) for its installation.

• Internet connection;

  This is required to allow TaxOnTree to retrieve sequence and taxonomic information via REST request from NCBI or Uniprot servers.

• OpenSSL;

  OpenSSL package is required by TaxOnTree to communicate with NCBI server which uses HTTPS communication protocol. Run the command openssl version to verify if it is installed in your system. If not, use the installation tool of your Unix distribution for its installation (sudo apt-get install libssl-dev for Debian or sudo yum install openssl-dev for RPM based distribution).

• FigTree.

  A free graphical phylogenetic trees viewer developed in Java by Andrew Rambaut group. TaxOnTree output is made to be visualized in this software. There are versions for MacOS, Linux and Windows. Pick the one that is more convenient for you.

Installation

> git clone https://github.com/tetsufmbio/taxontree.git
> cd taxontree
> ./install.sh  # Here you'll be asked for your email address.

NOTE: A valid email address is required for TaxOnTree execution to request data from other servers like NCBI and UniProt. The email address is requested by those servers admin to contact you when necessary. This could happen if you are using TaxOnTree excessively. To run TaxOnTree without internet connection, refer to the manual in docs folder.

This will install all TaxOnTree dependencies at $HOME/.taxontree/ folder, by default, and create an executable named taxontree. The installation process will also attempt to download and install some third-party software. This includes:

• MUSCLE;
• Clustal Omega;
• Kalign;
• trimAl;
• FastTree.

If some of them could not be installed, you can try to install them manually.

NOTE: Third-party software is only required when using TaxOnTree phylogenetic pipeline. If your input is a tree in Newick format, no third-party software is necessary.

Testing

If the installation goes well, it should create an executable called taxontree and display the following message after the command ./taxontree -version.

> ./taxontree -version

        TaxOnTree  Copyright (C) 2015-2020  Tetsu Sakamoto
        This program comes with ABSOLUTELY NO WARRANTY.
        This is free software, and you are welcome to redistribute it under
        certain conditions. See GNU general public license v.3 for details.

TaxOnTree v.1.10.1

A sample Newick file is also provided for test in sample folder. Try the following command:

> ./taxontree -treefile sample/test.nwk -queryid 544509544

This should generate a file called test_seq_tree.nex. Open this file on FigTree.

For more details on TaxOnTree command line usage, type the command ./taxontree -man or refer to the manual in docs folder.

Contact

If you have troubles installing TaxOnTree or suggestions to improve our work, please contact us by the following email address:

• [email protected] (Tetsu Sakamoto)
• [email protected] (J. Miguel Ortega)

Laboratório de Biodados
Instituto de Ciências Biológicas (ICB)
Universidade Federal de Minas Gerais (UFMG)
Belo Horizonte - Minas Gerais - BRAZIL
Zip code: 31270-010