SCORPiOs - Synteny-guided CORrection of Paralogies and Orthologies

SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event. SCORPiOs identifies gene trees where the whole-genome duplication is missing or incorrectly placed, based on the genomic locations of the duplicated genes across the different species. SCORPiOs then builds an optimized gene tree consistent with the known WGD event, the species tree, local synteny context, as well as gene sequence evolution.

SCORPiOs is implemented as a Snakemake pipeline. SCORPiOs takes as input either gene trees or multiple alignments, and outputs the corresponding optimized gene trees.

✨ New in SCORPiOs 2.0.0: LORelEi (Lineage-specific Ohnolog Resolution Extension)
SCORPiOs LORelEi analyzes sequence-synteny conflicts in gene trees and diagnose cases of delayed meiosis resolution following WGD. To learn how to use SCORPiOs and SCORPiOs LORelEi, take a look at SCORPiOs documentation!

If you use SCORPiOs, please cite:

Parey E, Louis A, Cabau C, Guiguen Y, Roest Crollius H, Berthelot C, Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications, Molecular Biology and Evolution, msaa149, https://doi.org/10.1093/molbev/msaa149.

Quick start

Below is a quick start guide to using SCORPiOs, we recommend reading SCORPiOs documentation for detailed instructions.

Table of content

• Installation
  • Installing conda
  • Installing SCORPiOs
• Usage
  • Setting up your working environment for SCORPiOs
  • Running SCORPiOs on example data
    • Example 1: Simple SCORPiOs run
    • Example 2: Iterative SCORPiOs run
  • Running SCORPiOS on your data
    • Preparing your configuration file
    • Running SCORPiOs
• Authors
• License
• References

Installation

Installing conda

The Miniconda3 package management system manages all SCORPiOs dependencies, including python packages and other software.

To install Miniconda3:

• Download Miniconda3 installer for your system here

• Run the installation script: bash Miniconda3-latest-Linux-x86_64.sh or bash Miniconda3-latest-MacOSX-x86_64.sh, and accept the defaults

• Open a new terminal, run conda update conda and press y to confirm updates

Installing SCORPiOs

• Clone the repository and go to SCORPiOs root folder

  git clone https://github.com/DyogenIBENS/SCORPIOS.git
  cd SCORPIOS
  

• Create the main conda environment.

  We recommend using Mamba for a faster installation:

  conda install -c conda-forge mamba
  mamba env create -f envs/scorpios.yaml
  

Updating SCORPiOs conda environment

• As of SCORPiOs v2.0.0, the conda environment was updated and needs to be reinstalled for users who have a previous version:

  conda env remove --name scorpios
  mamba env create -f envs/scorpios.yaml
  

Usage

Setting up your working environment for SCORPiOs

Before any SCORPiOs run, you should:

• go to SCORPiOs root folder,
• activate the conda environment with conda activate scorpios.

Running SCORPiOs on example data

Before using SCORPiOs on your data, we recommend running a test with our example data to ensure that installation was successful and to get familiar with the pipeline, inputs and outputs.

Example 1: Simple SCORPiOs run

SCORPiOs uses a YAML configuration file to specify inputs and parameters for each run. An example configuration file is provided: config_example.yaml. This configuration file executes SCORPiOs on toy example data located in data/example/, that you can use as reference for input formats.

The only required snakemake arguments to run SCORPiOs are --configfile, the --use-conda flag abd the --scheduler=greedy option. You also need to specify the number of threads via --cores. For more advanced options, you can look at the Snakemake documentation.

To run SCORPiOs on example data:

snakemake --configfile config_example.yaml --use-conda --cores 4 --scheduler=greedy

The following output should be generated: SCORPiOs_example/SCORPiOs_output_0.nhx.

Example 2: Iterative SCORPiOs run

SCORPiOs can run in iterative mode: SCORPiOs improves the gene trees a first time, and then uses the corrected set of gene trees again as input for a new correction run, until convergence. Correcting gene trees improves orthologies accuracy, which in turn makes synteny conservation patterns more informative, improving the gene tree reconstructions after successive runs. Usually, a small number of iterations (2-3) suffice to reach convergence.

To run SCORPiOs in iterative mode on example data, execute the wrapper bash script iterate_scorpios.sh:

bash iterate_scorpios.sh --snake_args="--configfile config_example.yaml --cores 4 --scheduler=greedy"

Command-line arguments:

Required
--snake_args="SNAKEMAKE ARGUMENTS", should at minimum contain --configfile

Optional
--max_iter=MAXITER, maximum number of iterations to run, default=5.
--min_corr=MINCORR, minimum number of corrected sub-trees to continue to the next iteration, default=1.
--starting_iter=ITER, starting iteration, to resume a run at a given iteration, default=1.

The following output should be generated: SCORPiOs_example/SCORPiOs_output_2_with_tags.nhx.

Running SCORPiOs on your data

Preparing your configuration file

To run SCORPiOs on your data, you have to create a new configuration file for your SCORPiOs run. You will need to format your input data adequately and write your configuration file, using the provided example config_example.yaml as a guide.

• Copy the example config file cp config_example.yaml config.yaml
• Open and edit config.yaml to specify paths, files and parameters for your data

To check your configuration, you can execute a dry-run with -n.

snakemake --configfile config.yaml --use-conda -n

Running SCORPiOs

Finally, you can run SCORPiOs as described above:

snakemake --configfile config.yaml --use-conda --cores 4 --scheduler=greedy

or in iterative mode:

bash iterate_scorpios.sh --snake_args="--configfile config.yaml --cores 4 --scheduler=greedy"

Authors

• Elise Parey
• Alexandra Louis
• Hugues Roest Crollius
• Camille Berthelot

License

This code may be freely distributed and modified under the terms of the GNU General Public License version 3 (GPL v3)

• LICENSE GPLv3

References

SCORPiOs uses the following tools to build and test gene trees:

• ProfileNJ: Noutahi et al. (2016) Efficient Gene Tree Correction Guided by Genome Evolution. PLOS ONE, 11, e0159559.

• RAxML: Stamatakis (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313.

• PhyML: Guindon et al. (2010) New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Syst Biol, 59, 307–321.

• TreeBeST: Vilella et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327–335.

• CONSEL: Shimodaira and Hasegawa (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics, 17, 1246–1247.