v2.0.0

What's Changed

• Bugfix: fixed bug in generation of simulated count profiles for calculating complementary log-likelihood ratio test (cLRT) background distributions
• Test False WGMs: implemented cLRTs for unsupported ("False") WGMs in addition to supported ("True") WGMs
• Benjamini-Hochberg FDR correction: implemented Benjamini-Hochberg FDR correction of cLRT p-values
• Test for a single WGM: the cLRT workflow is executed only on a single WGM, instead of on all WGMs listed in the input file.
• Remove consecutive WGMs: added code for handling the removal of one WGM on a branch containing several (max 3) WGMs
• CLI implementation: the cLRT workflow is available as a JAVA command line tool
• Minor: code efficiency improvements

Developed by Cecilia Sensalari and Dr. Steven Maere based on v2.0.0-dev by Setareh Tasdighian (in preprint, 2025)

v2.0.0-dev

Title:
First version of birth-death modeling of gene family evolution extended to include reverse engineering WGMs using a complementary log-likelihood ratio test pipeline

Tasdighian_Setareh.pdf

The birth-death modeling of gene family evolution was used to identify a set of gene families that expand almost exclusively through Whole Genome Multiplications (WGMs). These gene families are referred to as Reciprocally Retained (RR). More details on this model can be found in Tasdighian et al. 2017.

Version 1.0.0 was previously released on VIB-PSB GitHub.

What’s New in This Release?

This version extends the model by incorporating the Complementary Log-Likelihood Ratio Test (cLRT), introduced in Chapter 4 of my PhD thesis. The cLRT pipeline utilizes Reciprocally Retained (RR) gene families to infer the presence of WGMs on a phylogeny.

This is the initial implementation of the cLRT pipeline. While the code is fully functional, it is an earlier version that will be improved and structured more clearly in future updates.

For a detailed list of changes, see the

Full Changelog: https://github.com/stasdigh/BirthDeathModel/commits/v2.0.0-initial

Author & Contact

Developed by Setareh Tasdighian.
For inquiries, please reach out via GitHub or LinkedIn.

Code v1.0.0 as submitted alongside the article

Initial commit