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. Real Primates gene trees are analyzed to identify what characteristics of a gene tree are related to the precision of dating; 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.RequirementsThis 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.本基准集针对单基因树（single gene trees）单独开展分子钟定年（molecular clock dating）相关测试，其研究结果已发表于Guillaume Louvel与Hugues Roest Crollius撰写的"Factors influencing the accuracy and precision in dating single gene trees"（《影响单基因树定年精度与准度的相关因素》）一文。 本基准集通过分析真实灵长类（Primates）单基因树，以识别与定年精度相关的基因树特征；同时在灵长类物种树上模拟序列联配（sequence alignment），以在速率变异程度、联配长度等可控参数下测定定年的准度。 #### 数据集内容 1. `Louvel_Accuracy-dating_results_2024.tar.gz`： - `notebook/`：基于Python编写的统计分析脚本； - `outputs/`：包含分析所得图表与表格的HTML分析报告； - `lib/`：项目所需的依赖库； - `data/`：最终分析所需的中间数据（涵盖定年结果、基因树特征）； 2. `Louvel_Accuracy-dating_dating-source_2024.tar.gz`： - `dating-source/`：用于复现数据集所需的输入数据与配置文件； 3. `Louvel_Accuracy-dating_raw-data-preparation_2024.tar.gz`： - `raw-data-preparation/`：原始数据与生成`dating-source`数据集的完整步骤； #### 依赖要求 本代码需使用本项目实验室开发的专属库，这些库可从`github.com/DyogenIBENS/`获取，同时本包的`lib/`目录中也已附带所需依赖。具体依赖包括： - `Phylorgs` - `LibsDyogen_py3` - `ToolsDyogen_py3`