Code and data for molecular dating benchmark based on real and simulated Primates gene trees

Benchmark of molecular clock dating applied to single gene trees separately, whose results are described in “Factors influencing the accuracy and precision in dating single gene trees” by Guillaume Louvel and Hugues Roest Crollius.

1. Real Primates gene trees are analyzed to identify what characteristics of a gene tree are related to the precision of dating; 
2. alignments are also simulated on the tree of Primates to measure the accuracy of dating under controlled parameters such as the degree of rate variation and the length of the alignment.

Content

Louvel_Accuracy-dating_results_2024.tar.gz:
    - notebook/: statistical analyses in Python;
    - outputs/: html reports with figures/tables resulting from the analysis;
    - lib/: required libraries.
    - data/: intermediate data needed for the final analysis (dates, gene tree features);

Louvel_Accuracy-dating_dating-source_2024.tar.gz:
    - dating-source/: input data and config files necessary to reproduce data;

Louvel_Accuracy-dating_raw-data-preparation_2024.tar.gz:
    - raw-data-preparation/: raw data and steps to produce dating-source.

Requirements

This code requires the libraries developed in the lab for this project,
available at github.com/DyogenIBENS/, but also included here in lib/.

- Phylorgs
- LibsDyogen_py3
- ToolsDyogen_py3.