Copyright (C) 2020 INRIA

This program is released under the GNU Affero General Public License Version 3.0-or-later.

Treerecs

Treerecs is an open-source (species- and gene-) tree reconciliation software available for Linux, Windows and MacOS. It can correct, rearrange and (re-)root gene trees with regard to a given species tree.

This README contains condensed information about how to install and how to use Treerecs. For detailed information, please visit the website.

Installation

Binaries

The simplest way to get Treerecs is to download the precompiled binaries.

GNU/Linux and OS X

install treerecs with bioconda

Windows

We advise windows users to run Treerecs via Seaview. Install and launch Seaview, then open a gene tree file (for instance one of those provided in the examples) and choose “Reconcile->Reconcile, root and rearrange with Treerecs” in the menu.

If you want to use Treerecs without Seaview, you can download binaries from the gitlab page or find the latest version (1.2) here: treerecs.exe

From source

1. Get the source

Latest stable release:

• download zip
• downoad tar.gz

Development version (unstable)

• download zip
• downoad tar.gz

2. Build

cmake -DCMAKE_BUILD_TYPE=Release .
make

The created executable can be found in the bin directory.

./bin/treerecs -h

Note for Mac users:

The -P | --parallelize option requires the compiler to support openmp, which may not be the case for the default compiler. Consider using another compiler instead.

3. Install (optional)

sudo make install

If you ever wish to uninstall Treerecs:

sudo make uninstall

Usage

Syntax

• treerecs -h or --help
• treerecs -V or --version
• treerecs --usage
• treerecs -g GENETREE_FILE -s SPECIESTREE_FILE [-S SMAP_FILE] [-t BRANCH_SUPPORT_THRESHOLD] [...]
• treerecs -g GENETREE_FILE --info

For option details, please visit this page.

Tutorial

A tutorial is available at https://project.inria.fr/treerecs/tutorial/

References

• Treerecs: an integrated phylogenetic tool, from sequences to reconciliations (2020), Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Celine Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier, David P. Parsons (in press)
• Efficient Gene Tree Correction Guided by Genome Evolution (2016), Emmanuel Noutahi, Magali Semeria, Manuel Lafond, Jonathan Seguin, Bastien Boussau, Laurent Guéguen, Nadia El-Mabrouk,…
• An Optimal Reconciliation Algorithm for Gene Trees with Polytomies, Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk
• Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, Gergely J. Szöllősi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin, Bastien Boussau