Change Log

All notable changes to SCORPiOs, added after the first released version v1.0.0, will be documented here.

[Version 2.0.0] - 13/12/2021 - v2.0.0

Introducing SCORPiOs LORelEi (Lineage-specific Ohnolog Resolution Extension), an extension to SCORPiOs to detect LORe. Note that the scorpios environment has to be updated and that additional snakemake arguments are required to run scorpios (–scheduler=greedy and –cores, see the docs for updated usage instructions).

Added

  • SCORPiOs LORelEi (LORe Extension): an extension to diagnose potential cases of lineage-specific rediploidisation.

  • New experimental option to recompute branch-lengths with RAxML after all subtrees corrections (instead of treebest phyml).

  • Removed the deprecated --buffer_size argument from the configuration file.

  • Sphinx autodoc for the API.

Changed

  • Updated SCORPiOs conda environment to snakemake version 6.6.1 and added dependency to the roman python package.

[Version 1.3.0] - 23/11/2020 - v1.3.0

Further workflow updates to improve computational efficiency and simplify its usage. Note that the main conda environnment has been updated and needs to be reinstalled if you have the previous version.

Added

  • Default output trees in iterative mode have now tags for corrected internal WGD nodes (in addition to corresponding descending leaves).

Changed

  • RAxML replaces PhyML to compute site likelihood (CONSEL input for likelihood AU-tests).

  • Simplified usage for iterative correction: the wrapper script directly parses the YAML configuration file so that providing the jobname is no longer required (see the updated usage instructions).

Version 1.2.0 - 18/10/2020 - v1.2.0

Minor workflow updates to improve computational efficiency and scalability to large datasets.

Added

  • Option to perform community detection with spectral clustering instead of Girvan-Newman, for improved computational effciency on large datasets. (See the documentation for usage instructions).

Changed

  • treebest distmat now replaces fastdist to build input distance matrices for profileNJ.

  • Installation instructions now recommend mamba for a faster dependency solving process.

Version 1.1.0 - 19/05/2020 - v1.1.0

Developed a new visualization tool to inspect tree corrections.

Added

  • New tool to generate .png images for corrected trees.

  • New html documentation.

Fixed

  • Fixed high memory usage in subtrees reinsertion step.

  • Minor python code speed-ups.