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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
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.